1 package Text::Tradition::Collation;
3 use Encode qw( decode_utf8 );
6 use IPC::Run qw( run binary );
8 use Text::Tradition::Collation::Reading;
9 use Text::Tradition::Collation::RelationshipStore;
10 use Text::Tradition::Error;
12 use XML::LibXML::XPathContext;
18 default => sub { Graph->new() },
26 isa => 'Text::Tradition::Collation::RelationshipStore',
28 relationships => 'relationships',
29 related_readings => 'related_readings',
31 writer => '_set_relations',
36 isa => 'Text::Tradition',
41 isa => 'HashRef[Text::Tradition::Collation::Reading]',
45 _add_reading => 'set',
46 del_reading => 'delete',
47 has_reading => 'exists',
50 default => sub { {} },
53 has 'wit_list_separator' => (
62 default => 'base text',
79 isa => 'Text::Tradition::Collation::Reading',
80 writer => '_set_start',
86 isa => 'Text::Tradition::Collation::Reading',
94 predicate => 'has_cached_svg',
95 clearer => 'wipe_svg',
100 Text::Tradition::Collation - a software model for a text collation
105 my $t = Text::Tradition->new(
106 'name' => 'this is a text',
108 'file' => '/path/to/tei_parallel_seg_file.xml' );
110 my $c = $t->collation;
111 my @readings = $c->readings;
112 my @paths = $c->paths;
113 my @relationships = $c->relationships;
115 my $svg_variant_graph = $t->collation->as_svg();
119 Text::Tradition is a library for representation and analysis of collated
120 texts, particularly medieval ones. The Collation is the central feature of
121 a Tradition, where the text, its sequence of readings, and its relationships
122 between readings are actually kept.
128 The constructor. Takes a hash or hashref of the following arguments:
132 =item * tradition - The Text::Tradition object to which the collation
135 =item * linear - Whether the collation should be linear; that is, whether
136 transposed readings should be treated as two linked readings rather than one,
137 and therefore whether the collation graph is acyclic. Defaults to true.
139 =item * baselabel - The default label for the path taken by a base text
140 (if any). Defaults to 'base text'.
142 =item * wit_list_separator - The string to join a list of witnesses for
143 purposes of making labels in display graphs. Defaults to ', '.
145 =item * ac_label - The extra label to tack onto a witness sigil when
146 representing another layer of path for the given witness - that is, when
147 a text has more than one possible reading due to scribal corrections or
148 the like. Defaults to ' (a.c.)'.
158 =head2 wit_list_separator
164 Simple accessors for collation attributes.
168 The meta-reading at the start of every witness path.
172 The meta-reading at the end of every witness path.
176 Returns all Reading objects in the graph.
178 =head2 reading( $id )
180 Returns the Reading object corresponding to the given ID.
182 =head2 add_reading( $reading_args )
184 Adds a new reading object to the collation.
185 See L<Text::Tradition::Collation::Reading> for the available arguments.
187 =head2 del_reading( $object_or_id )
189 Removes the given reading from the collation, implicitly removing its
190 paths and relationships.
192 =head2 merge_readings( $main, $second )
194 Merges the $second reading into the $main one.
195 The arguments may be either readings or reading IDs.
197 =head2 has_reading( $id )
199 Predicate to see whether a given reading ID is in the graph.
201 =head2 reading_witnesses( $object_or_id )
203 Returns a list of sigils whose witnesses contain the reading.
207 Returns all reading paths within the document - that is, all edges in the
208 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
210 =head2 add_path( $source, $target, $sigil )
212 Links the given readings in the collation in sequence, under the given witness
213 sigil. The readings may be specified by object or ID.
215 =head2 del_path( $source, $target, $sigil )
217 Links the given readings in the collation in sequence, under the given witness
218 sigil. The readings may be specified by object or ID.
220 =head2 has_path( $source, $target );
222 Returns true if the two readings are linked in sequence in any witness.
223 The readings may be specified by object or ID.
227 Returns all Relationship objects in the collation.
229 =head2 add_relationship( $reading, $other_reading, $options )
231 Adds a new relationship of the type given in $options between the two readings,
232 which may be specified by object or ID. Returns a value of ( $status, @vectors)
233 where $status is true on success, and @vectors is a list of relationship edges
234 that were ultimately added.
235 See L<Text::Tradition::Collation::Relationship> for the available options.
241 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
242 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
243 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
246 ### Reading construct/destruct functions
249 my( $self, $reading ) = @_;
250 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
251 my %args = %$reading;
252 $reading = Text::Tradition::Collation::Reading->new(
253 'collation' => $self,
256 # First check to see if a reading with this ID exists.
257 if( $self->reading( $reading->id ) ) {
258 throw( "Collation already has a reading with id " . $reading->id );
260 $self->_add_reading( $reading->id => $reading );
261 # Once the reading has been added, put it in both graphs.
262 $self->sequence->add_vertex( $reading->id );
263 $self->relations->add_reading( $reading->id );
267 around del_reading => sub {
272 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
275 # Remove the reading from the graphs.
276 $self->sequence->delete_vertex( $arg );
277 $self->relations->delete_reading( $arg );
280 $self->$orig( $arg );
283 # merge_readings( $main, $to_be_deleted );
288 # We only need the IDs for adding paths to the graph, not the reading
289 # objects themselves.
290 my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
292 # The kept reading should inherit the paths and the relationships
293 # of the deleted reading.
294 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
295 my @vector = ( $kept );
296 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
297 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
298 next if $vector[0] eq $vector[1]; # Don't add a self loop
299 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
300 $self->sequence->add_edge( @vector );
301 my $fwits = $self->sequence->get_edge_attributes( @vector );
302 @wits{keys %$fwits} = values %$fwits;
303 $self->sequence->set_edge_attributes( @vector, \%wits );
305 $self->relations->merge_readings( $kept, $deleted, $combine_char );
307 # Do the deletion deed.
308 if( $combine_char ) {
309 my $kept_obj = $self->reading( $kept );
310 my $new_text = join( $combine_char, $kept_obj->text,
311 $self->reading( $deleted )->text );
312 $kept_obj->alter_text( $new_text );
314 $self->del_reading( $deleted );
318 # Helper function for manipulating the graph.
319 sub _stringify_args {
320 my( $self, $first, $second, $arg ) = @_;
322 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
323 $second = $second->id
324 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
325 return( $first, $second, $arg );
328 # Helper function for manipulating the graph.
329 sub _objectify_args {
330 my( $self, $first, $second, $arg ) = @_;
331 $first = $self->reading( $first )
332 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
333 $second = $self->reading( $second )
334 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
335 return( $first, $second, $arg );
342 # We only need the IDs for adding paths to the graph, not the reading
343 # objects themselves.
344 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
346 # Connect the readings
347 $self->sequence->add_edge( $source, $target );
348 # Note the witness in question
349 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
355 if( ref( $_[0] ) eq 'ARRAY' ) {
362 # We only need the IDs for adding paths to the graph, not the reading
363 # objects themselves.
364 my( $source, $target, $wit ) = $self->_stringify_args( @args );
366 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
367 $self->sequence->delete_edge_attribute( $source, $target, $wit );
369 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
370 $self->sequence->delete_edge( $source, $target );
375 # Extra graph-alike utility
378 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
379 return undef unless $self->sequence->has_edge( $source, $target );
380 return $self->sequence->has_edge_attribute( $source, $target, $wit );
383 =head2 clear_witness( @sigil_list )
385 Clear the given witnesses out of the collation entirely, removing references
386 to them in paths, and removing readings that belong only to them. Should only
387 be called via $tradition->del_witness.
392 my( $self, @sigils ) = @_;
394 # Clear the witness(es) out of the paths
395 foreach my $e ( $self->paths ) {
396 foreach my $sig ( @sigils ) {
397 $self->del_path( $e, $sig );
401 # Clear out the newly unused readings
402 foreach my $r ( $self->readings ) {
403 unless( $self->reading_witnesses( $r ) ) {
404 $self->del_reading( $r );
409 sub add_relationship {
411 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
412 my( @vectors ) = $self->relations->add_relationship( $source,
413 $self->reading( $source ), $target, $self->reading( $target ), $opts );
414 # Force a full rank recalculation every time. Yuck.
415 $self->calculate_ranks() if $self->end->has_rank;
419 =head2 reading_witnesses( $reading )
421 Return a list of sigils corresponding to the witnesses in which the reading appears.
425 sub reading_witnesses {
426 my( $self, $reading ) = @_;
427 # We need only check either the incoming or the outgoing edges; I have
428 # arbitrarily chosen "incoming". Thus, special-case the start node.
429 if( $reading eq $self->start ) {
430 return map { $_->sigil } $self->tradition->witnesses;
433 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
434 my $wits = $self->sequence->get_edge_attributes( @$e );
435 @all_witnesses{ keys %$wits } = 1;
437 return keys %all_witnesses;
440 =head1 OUTPUT METHODS
442 =head2 as_svg( \%options )
444 Returns an SVG string that represents the graph, via as_dot and graphviz.
445 See as_dot for a list of options.
450 my( $self, $opts ) = @_;
451 my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
452 if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
453 my @cmd = qw/dot -Tsvg/;
455 my $dotfile = File::Temp->new();
457 # $dotfile->unlink_on_destroy(0);
458 binmode $dotfile, ':utf8';
459 print $dotfile $self->as_dot( $opts );
460 push( @cmd, $dotfile->filename );
461 run( \@cmd, ">", binary(), \$svg );
462 $svg = decode_utf8( $svg );
463 $self->cached_svg( $svg ) unless $want_subgraph;
466 return $self->cached_svg;
471 =head2 as_dot( \%options )
473 Returns a string that is the collation graph expressed in dot
474 (i.e. GraphViz) format. Options include:
489 my( $self, $opts ) = @_;
490 my $startrank = $opts->{'from'} if $opts;
491 my $endrank = $opts->{'to'} if $opts;
492 my $color_common = $opts->{'color_common'} if $opts;
493 my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
494 && $self->end->rank > 100;
496 # Check the arguments
498 return if $endrank && $startrank > $endrank;
499 return if $startrank > $self->end->rank;
501 if( defined $endrank ) {
502 return if $endrank < 0;
503 $endrank = undef if $endrank == $self->end->rank;
506 my $graph_name = $self->tradition->name;
507 $graph_name =~ s/[^\w\s]//g;
508 $graph_name = join( '_', split( /\s+/, $graph_name ) );
516 'fillcolor' => 'white',
521 'arrowhead' => 'open',
522 'color' => '#000000',
523 'fontcolor' => '#000000',
526 my $dot = sprintf( "digraph %s {\n", $graph_name );
527 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
528 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
530 # Output substitute start/end readings if necessary
532 $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
535 $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
537 if( $STRAIGHTENHACK ) {
539 $dot .= "\tsubgraph { rank=same \"#START#\" \"#SILENT#\" }\n";
540 $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
542 my %used; # Keep track of the readings that actually appear in the graph
543 # Sort the readings by rank if we have ranks; this speeds layout.
544 my @all_readings = $self->end->has_rank
545 ? sort { $a->rank <=> $b->rank } $self->readings
547 # TODO Refrain from outputting lacuna nodes - just grey out the edges.
548 foreach my $reading ( @all_readings ) {
549 # Only output readings within our rank range.
550 next if $startrank && $reading->rank < $startrank;
551 next if $endrank && $reading->rank > $endrank;
552 $used{$reading->id} = 1;
553 # Need not output nodes without separate labels
554 next if $reading->id eq $reading->text;
556 my $label = $reading->text;
557 $label =~ s/\"/\\\"/g;
558 $rattrs->{'label'} = $label;
559 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
560 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
563 # Add the real edges. Need to weight one edge per rank jump, in a
565 # my $weighted = $self->_add_edge_weights;
566 my @edges = $self->paths;
567 my( %substart, %subend );
568 foreach my $edge ( @edges ) {
569 # Do we need to output this edge?
570 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
571 my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
572 my $variables = { %edge_attrs, 'label' => $label };
574 # Account for the rank gap if necessary
575 my $rank0 = $self->reading( $edge->[0] )->rank
576 if $self->reading( $edge->[0] )->has_rank;
577 my $rank1 = $self->reading( $edge->[1] )->rank
578 if $self->reading( $edge->[1] )->has_rank;
579 if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
580 $variables->{'minlen'} = $rank1 - $rank0;
583 # Add the calculated edge weights
584 # if( exists $weighted->{$edge->[0]}
585 # && $weighted->{$edge->[0]} eq $edge->[1] ) {
586 # # $variables->{'color'} = 'red';
587 # $variables->{'weight'} = 3.0;
590 # EXPERIMENTAL: make edge width reflect no. of witnesses
591 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
592 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
594 my $varopts = _dot_attr_string( $variables );
595 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
596 $edge->[0], $edge->[1], $varopts );
597 } elsif( $used{$edge->[0]} ) {
598 $subend{$edge->[0]} = 1;
599 } elsif( $used{$edge->[1]} ) {
600 $substart{$edge->[1]} = 1;
603 # Add substitute start and end edges if necessary
604 foreach my $node ( keys %substart ) {
605 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
606 my $variables = { %edge_attrs, 'label' => $witstr };
607 my $varopts = _dot_attr_string( $variables );
608 $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
610 foreach my $node ( keys %subend ) {
611 my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
612 my $variables = { %edge_attrs, 'label' => $witstr };
613 my $varopts = _dot_attr_string( $variables );
614 $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
617 if( $STRAIGHTENHACK ) {
618 $dot .= "\t\"#END#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
625 sub _dot_attr_string {
628 foreach my $k ( sort keys %$hash ) {
630 push( @attrs, $k.'="'.$v.'"' );
632 return( '[ ' . join( ', ', @attrs ) . ' ]' );
635 sub _add_edge_weights {
637 # Walk the graph from START to END, choosing the successor node with
638 # the largest number of witness paths each time.
640 my $curr = $self->start->id;
641 my $ranked = $self->end->has_rank;
642 while( $curr ne $self->end->id ) {
643 my $rank = $ranked ? $self->reading( $curr )->rank : 0;
644 my @succ = sort { $self->path_witnesses( $curr, $a )
645 <=> $self->path_witnesses( $curr, $b ) }
646 $self->sequence->successors( $curr );
647 my $next = pop @succ;
648 my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
649 # Try to avoid lacunae in the weighted path.
651 ( $self->reading( $next )->is_lacuna ||
652 $nextrank - $rank > 1 ) ){
655 $weighted->{$curr} = $next;
661 =head2 path_witnesses( $edge )
663 Returns the list of sigils whose witnesses are associated with the given edge.
664 The edge can be passed as either an array or an arrayref of ( $source, $target ).
669 my( $self, @edge ) = @_;
670 # If edge is an arrayref, cope.
671 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
675 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
679 sub _path_display_label {
682 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
683 if( scalar @wits > $maj ) {
684 # TODO break out a.c. wits
687 return join( ', ', @wits );
694 Returns a GraphML representation of the collation. The GraphML will contain
695 two graphs. The first expresses the attributes of the readings and the witness
696 paths that link them; the second expresses the relationships that link the
697 readings. This is the native transfer format for a tradition.
706 my $datafile = 't/data/florilegium_tei_ps.xml';
707 my $tradition = Text::Tradition->new( 'input' => 'TEI',
712 ok( $tradition, "Got a tradition object" );
713 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
714 ok( $tradition->collation, "Tradition has a collation" );
716 my $c = $tradition->collation;
717 is( scalar $c->readings, $READINGS, "Collation has all readings" );
718 is( scalar $c->paths, $PATHS, "Collation has all paths" );
719 is( scalar $c->relationships, 0, "Collation has all relationships" );
721 # Add a few relationships
722 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
723 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
724 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
726 # Now write it to GraphML and parse it again.
728 my $graphml = $c->as_graphml;
729 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
730 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
731 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
732 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
742 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
743 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
744 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
745 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
747 # Create the document and root node
748 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
749 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
750 $graphml->setDocumentElement( $root );
751 $root->setNamespace( $xsi_ns, 'xsi', 0 );
752 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
754 # Add the data keys for the graph
757 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
758 foreach my $datum ( @graph_attributes ) {
759 $graph_data_keys{$datum} = 'dg'.$gdi++;
760 my $key = $root->addNewChild( $graphml_ns, 'key' );
761 $key->setAttribute( 'attr.name', $datum );
762 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
763 $key->setAttribute( 'for', 'graph' );
764 $key->setAttribute( 'id', $graph_data_keys{$datum} );
767 # Add the data keys for nodes
774 is_start => 'boolean',
776 is_lacuna => 'boolean',
778 foreach my $datum ( keys %node_data ) {
779 $node_data_keys{$datum} = 'dn'.$ndi++;
780 my $key = $root->addNewChild( $graphml_ns, 'key' );
781 $key->setAttribute( 'attr.name', $datum );
782 $key->setAttribute( 'attr.type', $node_data{$datum} );
783 $key->setAttribute( 'for', 'node' );
784 $key->setAttribute( 'id', $node_data_keys{$datum} );
787 # Add the data keys for edges, i.e. witnesses
791 class => 'string', # Class, deprecated soon
792 witness => 'string', # ID/label for a path
793 relationship => 'string', # ID/label for a relationship
794 extra => 'boolean', # Path key
795 scope => 'string', # Relationship key
796 non_correctable => 'boolean', # Relationship key
797 non_independent => 'boolean', # Relationship key
799 foreach my $datum ( keys %edge_data ) {
800 $edge_data_keys{$datum} = 'de'.$edi++;
801 my $key = $root->addNewChild( $graphml_ns, 'key' );
802 $key->setAttribute( 'attr.name', $datum );
803 $key->setAttribute( 'attr.type', $edge_data{$datum} );
804 $key->setAttribute( 'for', 'edge' );
805 $key->setAttribute( 'id', $edge_data_keys{$datum} );
808 # Add the collation graph itself
809 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
810 $sgraph->setAttribute( 'edgedefault', 'directed' );
811 $sgraph->setAttribute( 'id', $self->tradition->name );
812 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
813 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
814 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
815 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
816 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
818 # Collation attribute data
819 foreach my $datum ( @graph_attributes ) {
820 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
821 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
826 # Add our readings to the graph
827 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
828 # Add to the main graph
829 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
830 my $node_xmlid = 'n' . $node_ctr++;
831 $node_hash{ $n->id } = $node_xmlid;
832 $node_el->setAttribute( 'id', $node_xmlid );
833 foreach my $d ( keys %node_data ) {
835 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
840 # Add the path edges to the sequence graph
842 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
843 # We add an edge in the graphml for every witness in $e.
844 foreach my $wit ( sort $self->path_witnesses( $e ) ) {
845 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
846 $node_hash{ $e->[0] },
847 $node_hash{ $e->[1] } );
848 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
849 $edge_el->setAttribute( 'source', $from );
850 $edge_el->setAttribute( 'target', $to );
851 $edge_el->setAttribute( 'id', $id );
853 # It's a witness path, so add the witness
855 my $key = $edge_data_keys{'witness'};
856 # Is this an ante-corr witness?
857 my $aclabel = $self->ac_label;
858 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
859 # Keep the base witness
861 # ...and record that this is an 'extra' reading path
862 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
864 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
865 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
869 # Add the relationship graph to the XML
870 $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
871 $node_data_keys{'id'}, \%edge_data_keys );
873 # Save and return the thing
874 my $result = decode_utf8( $graphml->toString(1) );
878 sub _add_graphml_data {
879 my( $el, $key, $value ) = @_;
880 return unless defined $value;
881 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
882 $data_el->setAttribute( 'key', $key );
883 $data_el->appendText( $value );
888 Returns a CSV alignment table representation of the collation graph, one
889 row per witness (or witness uncorrected.)
895 my $table = $self->make_alignment_table;
896 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
898 # Make the header row
899 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
900 push( @result, decode_utf8( $csv->string ) );
901 # Make the rest of the rows
902 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
903 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
904 my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
905 $csv->combine( @row );
906 push( @result, decode_utf8( $csv->string ) );
908 return join( "\n", @result );
911 =head2 make_alignment_table( $use_refs, $include_witnesses )
913 Return a reference to an alignment table, in a slightly enhanced CollateX
914 format which looks like this:
916 $table = { alignment => [ { witness => "SIGIL",
917 tokens => [ { t => "TEXT" }, ... ] },
919 tokens => [ { t => "TEXT" }, ... ] },
923 If $use_refs is set to 1, the reading object is returned in the table
924 instead of READINGTEXT; if not, the text of the reading is returned.
926 If $include_witnesses is set to a hashref, only the witnesses whose sigil
927 keys have a true hash value will be included.
931 sub make_alignment_table {
932 my( $self, $noderefs, $include ) = @_;
933 # Make sure we can do this
934 throw( "Need a linear graph in order to make an alignment table" )
935 unless $self->linear;
936 $self->calculate_ranks unless $self->end->has_rank;
938 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
939 my @all_pos = ( 1 .. $self->end->rank - 1 );
940 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
942 next unless $include->{$wit->sigil};
944 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
945 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
946 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
947 push( @{$table->{'alignment'}},
948 { 'witness' => $wit->sigil, 'tokens' => \@row } );
949 if( $wit->is_layered ) {
950 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
951 $wit->sigil.$self->ac_label );
952 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
953 push( @{$table->{'alignment'}},
954 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
960 sub _make_witness_row {
961 my( $path, $positions, $noderefs ) = @_;
963 map { $char_hash{$_} = undef } @$positions;
965 foreach my $rdg ( @$path ) {
966 my $rtext = $rdg->text;
967 $rtext = '#LACUNA#' if $rdg->is_lacuna;
968 print STDERR "rank " . $rdg->rank . "\n" if $debug;
969 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
970 $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
973 my @row = map { $char_hash{$_} } @$positions;
974 # Fill in lacuna markers for undef spots in the row
975 my $last_el = shift @row;
976 my @filled_row = ( $last_el );
977 foreach my $el ( @row ) {
978 # If we are using node reference, make the lacuna node appear many times
979 # in the table. If not, use the lacuna tag.
980 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
981 $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
983 push( @filled_row, $el );
989 # Tiny utility function to say if a table element is a lacuna
992 return 1 if $el->{'t'} eq '#LACUNA#';
993 return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
994 && $el->{'t'}->is_lacuna;
998 # Helper to turn the witnesses along columns rather than rows. Assumes
1003 return $result unless scalar @$table;
1004 my $nrows = scalar @{$table->[0]};
1005 foreach my $idx ( 0 .. $nrows - 1 ) {
1006 foreach my $wit ( 0 .. $#{$table} ) {
1007 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
1013 =head1 NAVIGATION METHODS
1015 =head2 reading_sequence( $first, $last, $sigil, $backup )
1017 Returns the ordered list of readings, starting with $first and ending
1018 with $last, for the witness given in $sigil. If a $backup sigil is
1019 specified (e.g. when walking a layered witness), it will be used wherever
1020 no $sigil path exists. If there is a base text reading, that will be
1021 used wherever no path exists for $sigil or $backup.
1025 # TODO Think about returning some lazy-eval iterator.
1026 # TODO Get rid of backup; we should know from what witness is whether we need it.
1028 sub reading_sequence {
1029 my( $self, $start, $end, $witness ) = @_;
1031 $witness = $self->baselabel unless $witness;
1032 my @readings = ( $start );
1035 while( $n && $n->id ne $end->id ) {
1036 if( exists( $seen{$n->id} ) ) {
1037 throw( "Detected loop for $witness at " . $n->id );
1041 my $next = $self->next_reading( $n, $witness );
1043 throw( "Did not find any path for $witness from reading " . $n->id );
1045 push( @readings, $next );
1048 # Check that the last reading is our end reading.
1049 my $last = $readings[$#readings];
1050 throw( "Last reading found from " . $start->text .
1051 " for witness $witness is not the end!" ) # TODO do we get this far?
1052 unless $last->id eq $end->id;
1057 =head2 next_reading( $reading, $sigil );
1059 Returns the reading that follows the given reading along the given witness
1065 # Return the successor via the corresponding path.
1067 my $answer = $self->_find_linked_reading( 'next', @_ );
1068 return undef unless $answer;
1069 return $self->reading( $answer );
1072 =head2 prior_reading( $reading, $sigil )
1074 Returns the reading that precedes the given reading along the given witness
1080 # Return the predecessor via the corresponding path.
1082 my $answer = $self->_find_linked_reading( 'prior', @_ );
1083 return $self->reading( $answer );
1086 sub _find_linked_reading {
1087 my( $self, $direction, $node, $path ) = @_;
1089 # Get a backup if we are dealing with a layered witness
1091 my $aclabel = $self->ac_label;
1092 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1096 my @linked_paths = $direction eq 'next'
1097 ? $self->sequence->edges_from( $node )
1098 : $self->sequence->edges_to( $node );
1099 return undef unless scalar( @linked_paths );
1101 # We have to find the linked path that contains all of the
1102 # witnesses supplied in $path.
1103 my( @path_wits, @alt_path_wits );
1104 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1105 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1108 foreach my $le ( @linked_paths ) {
1109 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1112 my @le_wits = sort $self->path_witnesses( $le );
1113 if( _is_within( \@path_wits, \@le_wits ) ) {
1114 # This is the right path.
1115 return $direction eq 'next' ? $le->[1] : $le->[0];
1116 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1120 # Got this far? Return the alternate path if it exists.
1121 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1124 # Got this far? Return the base path if it exists.
1125 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1128 # Got this far? We have no appropriate path.
1129 warn "Could not find $direction node from " . $node->id
1130 . " along path $path";
1136 my( $set1, $set2 ) = @_;
1137 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1138 foreach my $el ( @$set1 ) {
1139 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1144 # Return the string that joins together a list of witnesses for
1145 # display on a single path.
1146 sub _witnesses_of_label {
1147 my( $self, $label ) = @_;
1148 my $regex = $self->wit_list_separator;
1149 my @answer = split( /\Q$regex\E/, $label );
1153 =head2 common_readings
1155 Returns the list of common readings in the graph (i.e. those readings that are
1156 shared by all non-lacunose witnesses.)
1160 sub common_readings {
1162 my @common = grep { $_->is_common } $self->readings;
1166 =head2 path_text( $sigil, $mainsigil [, $start, $end ] )
1168 Returns the text of a witness (plus its backup, if we are using a layer)
1169 as stored in the collation. The text is returned as a string, where the
1170 individual readings are joined with spaces and the meta-readings (e.g.
1171 lacunae) are omitted. Optional specification of $start and $end allows
1172 the generation of a subset of the witness text.
1177 my( $self, $wit, $start, $end ) = @_;
1178 $start = $self->start unless $start;
1179 $end = $self->end unless $end;
1180 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1181 return join( ' ', map { $_->text } @path );
1184 =head1 INITIALIZATION METHODS
1186 These are mostly for use by parsers.
1188 =head2 make_witness_path( $witness )
1190 Link the array of readings contained in $witness->path (and in
1191 $witness->uncorrected_path if it exists) into collation paths.
1192 Clear out the arrays when finished.
1194 =head2 make_witness_paths
1196 Call make_witness_path for all witnesses in the tradition.
1200 # For use when a collation is constructed from a base text and an apparatus.
1201 # We have the sequences of readings and just need to add path edges.
1202 # When we are done, clear out the witness path attributes, as they are no
1204 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1206 sub make_witness_paths {
1208 foreach my $wit ( $self->tradition->witnesses ) {
1209 # print STDERR "Making path for " . $wit->sigil . "\n";
1210 $self->make_witness_path( $wit );
1214 sub make_witness_path {
1215 my( $self, $wit ) = @_;
1216 my @chain = @{$wit->path};
1217 my $sig = $wit->sigil;
1218 foreach my $idx ( 0 .. $#chain-1 ) {
1219 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1221 if( $wit->is_layered ) {
1222 @chain = @{$wit->uncorrected_path};
1223 foreach my $idx( 0 .. $#chain-1 ) {
1224 my $source = $chain[$idx];
1225 my $target = $chain[$idx+1];
1226 $self->add_path( $source, $target, $sig.$self->ac_label )
1227 unless $self->has_path( $source, $target, $sig );
1231 $wit->clear_uncorrected_path;
1234 =head2 calculate_ranks
1236 Calculate the reading ranks (that is, their aligned positions relative
1237 to each other) for the graph. This can only be called on linear collations.
1241 use Text::Tradition;
1243 my $cxfile = 't/data/Collatex-16.xml';
1244 my $t = Text::Tradition->new(
1246 'input' => 'CollateX',
1249 my $c = $t->collation;
1252 my $svg = $c->as_svg;
1253 is( substr( $svg, 0, 5 ), '<?xml', "Got XML doc for svg" );
1254 ok( $c->has_cached_svg, "SVG was cached" );
1255 is( $c->as_svg, $svg, "Cached SVG returned upon second call" );
1256 $c->calculate_ranks;
1257 is( $c->as_svg, $svg, "Cached SVG retained with no rank change" );
1258 $c->add_relationship( 'n9', 'n23', { 'type' => 'spelling' } );
1259 isnt( $c->as_svg, $svg, "SVG changed after relationship add" );
1265 sub calculate_ranks {
1267 # Save the existing ranks, in case we need to invalidate the cached SVG.
1269 # Walk a version of the graph where every node linked by a relationship
1270 # edge is fundamentally the same node, and do a topological ranking on
1271 # the nodes in this graph.
1272 my $topo_graph = Graph->new();
1276 foreach my $r ( $self->readings ) {
1277 next if exists $rel_containers{$r->id};
1278 my @rels = $r->related_readings( 'colocated' );
1280 # Make a relationship container.
1282 my $rn = 'rel_container_' . $rel_ctr++;
1283 $topo_graph->add_vertex( $rn );
1285 $rel_containers{$_->id} = $rn;
1288 # Add a new node to mirror the old node.
1289 $rel_containers{$r->id} = $r->id;
1290 $topo_graph->add_vertex( $r->id );
1295 foreach my $r ( $self->readings ) {
1296 $existing_ranks{$r} = $r->rank;
1297 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1298 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1299 $rel_containers{$n} );
1300 # $DB::single = 1 unless $tfrom && $tto;
1301 $topo_graph->add_edge( $tfrom, $tto );
1305 # Now do the rankings, starting with the start node.
1306 my $topo_start = $rel_containers{$self->start->id};
1307 my $node_ranks = { $topo_start => 0 };
1308 my @curr_origin = ( $topo_start );
1309 # A little iterative function.
1310 while( @curr_origin ) {
1311 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1313 # Transfer our rankings from the topological graph to the real one.
1314 foreach my $r ( $self->readings ) {
1315 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1316 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1318 # Die. Find the last rank we calculated.
1319 my @all_defined = sort { $node_ranks->{$rel_containers{$a->id}}
1320 <=> $node_ranks->{$rel_containers{$b->id}} }
1322 my $last = pop @all_defined;
1323 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1326 # Do we need to invalidate the cached SVG?
1327 if( $self->has_cached_svg ) {
1328 foreach my $r ( $self->readings ) {
1329 next if $existing_ranks{$r} == $r->rank;
1337 my( $graph, $node_ranks, @current_nodes ) = @_;
1338 # Look at each of the children of @current_nodes. If all the child's
1339 # parents have a rank, assign it the highest rank + 1 and add it to
1340 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1341 # parent gets a rank.
1343 foreach my $c ( @current_nodes ) {
1344 warn "Current reading $c has no rank!"
1345 unless exists $node_ranks->{$c};
1346 # print STDERR "Looking at child of node $c, rank "
1347 # . $node_ranks->{$c} . "\n";
1348 foreach my $child ( $graph->successors( $c ) ) {
1349 next if exists $node_ranks->{$child};
1350 my $highest_rank = -1;
1352 foreach my $parent ( $graph->predecessors( $child ) ) {
1353 if( exists $node_ranks->{$parent} ) {
1354 $highest_rank = $node_ranks->{$parent}
1355 if $highest_rank <= $node_ranks->{$parent};
1362 my $c_rank = $highest_rank + 1;
1363 # print STDERR "Assigning rank $c_rank to node $child \n";
1364 $node_ranks->{$child} = $c_rank;
1365 push( @next_nodes, $child );
1371 =head2 flatten_ranks
1373 A convenience method for parsing collation data. Searches the graph for readings
1374 with the same text at the same rank, and merges any that are found.
1380 my %unique_rank_rdg;
1381 foreach my $rdg ( $self->readings ) {
1382 next unless $rdg->has_rank;
1383 my $key = $rdg->rank . "||" . $rdg->text;
1384 if( exists $unique_rank_rdg{$key} ) {
1386 # print STDERR "Combining readings at same rank: $key\n";
1387 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1388 # TODO see if this now makes a common point.
1390 $unique_rank_rdg{$key} = $rdg;
1395 =head2 remove_collations
1397 Another convenience method for parsing. Removes all 'collation' relationships
1398 that were defined in order to get the reading ranks to be correct.
1402 use Text::Tradition;
1404 my $cxfile = 't/data/Collatex-16.xml';
1405 my $t = Text::Tradition->new(
1407 'input' => 'CollateX',
1410 my $c = $t->collation;
1412 isnt( $c->reading('n23')->rank, $c->reading('n9')->rank, "Rank skew exists" );
1413 $c->add_relationship( 'n23', 'n9', { 'type' => 'collated', 'scope' => 'local' } );
1414 is( scalar $c->relationships, 4, "Found all expected relationships" );
1415 $c->remove_collations;
1416 is( scalar $c->relationships, 3, "Collated relationships now gone" );
1417 is( $c->reading('n23')->rank, $c->reading('n9')->rank, "Aligned ranks were preserved" );
1423 sub remove_collations {
1425 foreach my $reledge ( $self->relationships ) {
1426 my $relobj = $self->relations->get_relationship( $reledge );
1427 if( $relobj && $relobj->type eq 'collated' ) {
1428 $self->relations->delete_relationship( $reledge );
1434 =head2 calculate_common_readings
1436 Goes through the graph identifying the readings that appear in every witness
1437 (apart from those with lacunae at that spot.) Marks them as common and returns
1442 use Text::Tradition;
1444 my $cxfile = 't/data/Collatex-16.xml';
1445 my $t = Text::Tradition->new(
1447 'input' => 'CollateX',
1450 my $c = $t->collation;
1452 my @common = $c->calculate_common_readings();
1453 is( scalar @common, 8, "Found correct number of common readings" );
1454 my @marked = sort $c->common_readings();
1455 is( scalar @common, 8, "All common readings got marked as such" );
1456 my @expected = qw/ n1 n12 n16 n19 n20 n5 n6 n7 /;
1457 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1463 sub calculate_common_readings {
1466 my $table = $self->make_alignment_table( 1 );
1467 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1468 my @row = map { $_->{'tokens'}->[$idx]->{'t'} } @{$table->{'alignment'}};
1470 foreach my $r ( @row ) {
1472 $hash{$r->id} = $r unless $r->is_meta;
1474 $hash{'UNDEF'} = $r;
1477 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1478 my( $r ) = values %hash;
1480 push( @common, $r );
1486 =head2 text_from_paths
1488 Calculate the text array for all witnesses from the path, for later consistency
1489 checking. Only to be used if there is no non-graph-based way to know the
1494 sub text_from_paths {
1496 foreach my $wit ( $self->tradition->witnesses ) {
1497 my @text = split( /\s+/,
1498 $self->reading_sequence( $self->start, $self->end, $wit->sigil ) );
1499 $wit->text( \@text );
1500 if( $wit->is_layered ) {
1501 my @uctext = split( /\s+/,
1502 $self->reading_sequence( $self->start, $self->end,
1503 $wit->sigil.$self->ac_label ) );
1504 $wit->text( \@uctext );
1509 =head1 UTILITY FUNCTIONS
1511 =head2 common_predecessor( $reading_a, $reading_b )
1513 Find the last reading that occurs in sequence before both the given readings.
1515 =head2 common_successor( $reading_a, $reading_b )
1517 Find the first reading that occurs in sequence after both the given readings.
1521 use Text::Tradition;
1523 my $cxfile = 't/data/Collatex-16.xml';
1524 my $t = Text::Tradition->new(
1526 'input' => 'CollateX',
1529 my $c = $t->collation;
1531 is( $c->common_predecessor( 'n9', 'n23' )->id,
1532 'n20', "Found correct common predecessor" );
1533 is( $c->common_successor( 'n9', 'n23' )->id,
1534 '#END#', "Found correct common successor" );
1536 is( $c->common_predecessor( 'n19', 'n17' )->id,
1537 'n16', "Found correct common predecessor for readings on same path" );
1538 is( $c->common_successor( 'n21', 'n26' )->id,
1539 '#END#', "Found correct common successor for readings on same path" );
1545 ## Return the closest reading that is a predecessor of both the given readings.
1546 sub common_predecessor {
1548 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1549 return $self->_common_in_path( $r1, $r2, 'predecessors' );
1552 sub common_successor {
1554 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1555 return $self->_common_in_path( $r1, $r2, 'successors' );
1558 sub _common_in_path {
1559 my( $self, $r1, $r2, $dir ) = @_;
1560 my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
1561 $iter = $self->end->rank - $iter if $dir eq 'successors';
1563 my @last_checked = ( $r1, $r2 );
1565 while( !@candidates ) {
1567 foreach my $lc ( @last_checked ) {
1568 foreach my $p ( $lc->$dir ) {
1569 if( $all_seen{$p->id} ) {
1570 push( @candidates, $p );
1572 $all_seen{$p->id} = 1;
1573 push( @new_lc, $p );
1577 @last_checked = @new_lc;
1579 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1580 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1584 Text::Tradition::Error->throw(
1585 'ident' => 'Collation error',
1591 __PACKAGE__->meta->make_immutable;
1595 This package is free software and is provided "as is" without express
1596 or implied warranty. You can redistribute it and/or modify it under
1597 the same terms as Perl itself.
1601 Tara L Andrews E<lt>aurum@cpan.orgE<gt>