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',
93 Text::Tradition::Collation - a software model for a text collation
98 my $t = Text::Tradition->new(
99 'name' => 'this is a text',
101 'file' => '/path/to/tei_parallel_seg_file.xml' );
103 my $c = $t->collation;
104 my @readings = $c->readings;
105 my @paths = $c->paths;
106 my @relationships = $c->relationships;
108 my $svg_variant_graph = $t->collation->as_svg();
112 Text::Tradition is a library for representation and analysis of collated
113 texts, particularly medieval ones. The Collation is the central feature of
114 a Tradition, where the text, its sequence of readings, and its relationships
115 between readings are actually kept.
121 The constructor. Takes a hash or hashref of the following arguments:
125 =item * tradition - The Text::Tradition object to which the collation
128 =item * linear - Whether the collation should be linear; that is, whether
129 transposed readings should be treated as two linked readings rather than one,
130 and therefore whether the collation graph is acyclic. Defaults to true.
132 =item * baselabel - The default label for the path taken by a base text
133 (if any). Defaults to 'base text'.
135 =item * wit_list_separator - The string to join a list of witnesses for
136 purposes of making labels in display graphs. Defaults to ', '.
138 =item * ac_label - The extra label to tack onto a witness sigil when
139 representing another layer of path for the given witness - that is, when
140 a text has more than one possible reading due to scribal corrections or
141 the like. Defaults to ' (a.c.)'.
151 =head2 wit_list_separator
157 Simple accessors for collation attributes.
161 The meta-reading at the start of every witness path.
165 The meta-reading at the end of every witness path.
169 Returns all Reading objects in the graph.
171 =head2 reading( $id )
173 Returns the Reading object corresponding to the given ID.
175 =head2 add_reading( $reading_args )
177 Adds a new reading object to the collation.
178 See L<Text::Tradition::Collation::Reading> for the available arguments.
180 =head2 del_reading( $object_or_id )
182 Removes the given reading from the collation, implicitly removing its
183 paths and relationships.
185 =head2 merge_readings( $main, $second )
187 Merges the $second reading into the $main one.
188 The arguments may be either readings or reading IDs.
190 =head2 has_reading( $id )
192 Predicate to see whether a given reading ID is in the graph.
194 =head2 reading_witnesses( $object_or_id )
196 Returns a list of sigils whose witnesses contain the reading.
200 Returns all reading paths within the document - that is, all edges in the
201 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
203 =head2 add_path( $source, $target, $sigil )
205 Links the given readings in the collation in sequence, under the given witness
206 sigil. The readings may be specified by object or ID.
208 =head2 del_path( $source, $target, $sigil )
210 Links the given readings in the collation in sequence, under the given witness
211 sigil. The readings may be specified by object or ID.
213 =head2 has_path( $source, $target );
215 Returns true if the two readings are linked in sequence in any witness.
216 The readings may be specified by object or ID.
220 Returns all Relationship objects in the collation.
222 =head2 add_relationship( $reading, $other_reading, $options )
224 Adds a new relationship of the type given in $options between the two readings,
225 which may be specified by object or ID. Returns a value of ( $status, @vectors)
226 where $status is true on success, and @vectors is a list of relationship edges
227 that were ultimately added.
228 See L<Text::Tradition::Collation::Relationship> for the available options.
234 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
235 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
236 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
239 ### Reading construct/destruct functions
242 my( $self, $reading ) = @_;
243 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
244 my %args = %$reading;
245 $reading = Text::Tradition::Collation::Reading->new(
246 'collation' => $self,
249 # First check to see if a reading with this ID exists.
250 if( $self->reading( $reading->id ) ) {
251 throw( "Collation already has a reading with id " . $reading->id );
253 $self->_add_reading( $reading->id => $reading );
254 # Once the reading has been added, put it in both graphs.
255 $self->sequence->add_vertex( $reading->id );
256 $self->relations->add_reading( $reading->id );
260 around del_reading => sub {
265 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
268 # Remove the reading from the graphs.
269 $self->sequence->delete_vertex( $arg );
270 $self->relations->delete_reading( $arg );
273 $self->$orig( $arg );
276 # merge_readings( $main, $to_be_deleted );
281 # We only need the IDs for adding paths to the graph, not the reading
282 # objects themselves.
283 my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
285 # The kept reading should inherit the paths and the relationships
286 # of the deleted reading.
287 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
288 my @vector = ( $kept );
289 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
290 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
291 next if $vector[0] eq $vector[1]; # Don't add a self loop
292 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
293 $self->sequence->add_edge( @vector );
294 my $fwits = $self->sequence->get_edge_attributes( @vector );
295 @wits{keys %$fwits} = values %$fwits;
296 $self->sequence->set_edge_attributes( @vector, \%wits );
298 $self->relations->merge_readings( $kept, $deleted, $combine_char );
300 # Do the deletion deed.
301 if( $combine_char ) {
302 my $kept_obj = $self->reading( $kept );
303 my $new_text = join( $combine_char, $kept_obj->text,
304 $self->reading( $deleted )->text );
305 $kept_obj->alter_text( $new_text );
307 $self->del_reading( $deleted );
311 # Helper function for manipulating the graph.
312 sub _stringify_args {
313 my( $self, $first, $second, $arg ) = @_;
315 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
316 $second = $second->id
317 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
318 return( $first, $second, $arg );
321 # Helper function for manipulating the graph.
322 sub _objectify_args {
323 my( $self, $first, $second, $arg ) = @_;
324 $first = $self->reading( $first )
325 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
326 $second = $self->reading( $second )
327 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
328 return( $first, $second, $arg );
335 # We only need the IDs for adding paths to the graph, not the reading
336 # objects themselves.
337 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
339 # Connect the readings
340 $self->sequence->add_edge( $source, $target );
341 # Note the witness in question
342 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
348 if( ref( $_[0] ) eq 'ARRAY' ) {
355 # We only need the IDs for adding paths to the graph, not the reading
356 # objects themselves.
357 my( $source, $target, $wit ) = $self->_stringify_args( @args );
359 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
360 $self->sequence->delete_edge_attribute( $source, $target, $wit );
362 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
363 $self->sequence->delete_edge( $source, $target );
368 # Extra graph-alike utility
371 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
372 return undef unless $self->sequence->has_edge( $source, $target );
373 return $self->sequence->has_edge_attribute( $source, $target, $wit );
376 =head2 clear_witness( @sigil_list )
378 Clear the given witnesses out of the collation entirely, removing references
379 to them in paths, and removing readings that belong only to them. Should only
380 be called via $tradition->del_witness.
385 my( $self, @sigils ) = @_;
387 # Clear the witness(es) out of the paths
388 foreach my $e ( $self->paths ) {
389 foreach my $sig ( @sigils ) {
390 $self->del_path( $e, $sig );
394 # Clear out the newly unused readings
395 foreach my $r ( $self->readings ) {
396 unless( $self->reading_witnesses( $r ) ) {
397 $self->del_reading( $r );
402 sub add_relationship {
404 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
405 my( @vectors ) = $self->relations->add_relationship( $source,
406 $self->reading( $source ), $target, $self->reading( $target ), $opts );
407 # Force a full rank recalculation every time. Yuck.
408 $self->calculate_ranks() if $self->end->has_rank;
412 =head2 reading_witnesses( $reading )
414 Return a list of sigils corresponding to the witnesses in which the reading appears.
418 sub reading_witnesses {
419 my( $self, $reading ) = @_;
420 # We need only check either the incoming or the outgoing edges; I have
421 # arbitrarily chosen "incoming". Thus, special-case the start node.
422 if( $reading eq $self->start ) {
423 return map { $_->sigil } $self->tradition->witnesses;
426 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
427 my $wits = $self->sequence->get_edge_attributes( @$e );
428 @all_witnesses{ keys %$wits } = 1;
430 return keys %all_witnesses;
433 =head1 OUTPUT METHODS
435 =head2 as_svg( \%options )
437 Returns an SVG string that represents the graph, via as_dot and graphviz.
438 See as_dot for a list of options.
443 my( $self, $opts ) = @_;
445 my @cmd = qw/dot -Tsvg/;
447 my $dotfile = File::Temp->new();
449 # $dotfile->unlink_on_destroy(0);
450 binmode $dotfile, ':utf8';
451 print $dotfile $self->as_dot( $opts );
452 push( @cmd, $dotfile->filename );
453 run( \@cmd, ">", binary(), \$svg );
454 # HACK part 3 - remove silent node+edge
455 my $parser = XML::LibXML->new();
456 my $svgdom = $parser->parse_string( $svg );
457 my $xpc = XML::LibXML::XPathContext->new( $svgdom->documentElement );
458 $xpc->registerNs( 'svg', 'http://www.w3.org/2000/svg' );
459 my @hacknodes = $xpc->findnodes( '//svg:g[contains(child::svg:title, "#SILENT#")]' );
460 foreach my $h ( @hacknodes ) {
461 $h->parentNode->removeChild( $h );
463 return decode_utf8( $svgdom->toString() );
467 =head2 as_dot( \%options )
469 Returns a string that is the collation graph expressed in dot
470 (i.e. GraphViz) format. Options include:
485 my( $self, $opts ) = @_;
486 my $startrank = $opts->{'from'} if $opts;
487 my $endrank = $opts->{'to'} if $opts;
488 my $color_common = $opts->{'color_common'} if $opts;
490 # Check the arguments
492 return if $endrank && $startrank > $endrank;
493 return if $startrank > $self->end->rank;
495 if( defined $endrank ) {
496 return if $endrank < 0;
497 $endrank = undef if $endrank == $self->end->rank;
500 # TODO consider making some of these things configurable
501 my $graph_name = $self->tradition->name;
502 $graph_name =~ s/[^\w\s]//g;
503 $graph_name = join( '_', split( /\s+/, $graph_name ) );
511 'fillcolor' => 'white',
516 'arrowhead' => 'open',
517 'color' => '#000000',
518 'fontcolor' => '#000000',
521 my $dot = sprintf( "digraph %s {\n", $graph_name );
522 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
523 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
525 # Output substitute start/end readings if necessary
527 $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
530 $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
532 if( !$startrank && !$endrank ) {
534 $dot .= "\tsubgraph { rank=same \"#START#\" \"#SILENT#\" }\n";
535 $dot .= "\t\"#SILENT#\" [ color=white,penwidth=0,label=\"\" ];"
537 my %used; # Keep track of the readings that actually appear in the graph
538 foreach my $reading ( $self->readings ) {
539 # Only output readings within our rank range.
540 next if $startrank && $reading->rank < $startrank;
541 next if $endrank && $reading->rank > $endrank;
542 $used{$reading->id} = 1;
543 # Need not output nodes without separate labels
544 next if $reading->id eq $reading->text;
546 my $label = $reading->text;
547 $label =~ s/\"/\\\"/g;
548 $rattrs->{'label'} = $label;
549 $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
550 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
554 my @edges = $self->paths;
555 my( %substart, %subend );
556 foreach my $edge ( @edges ) {
557 # Do we need to output this edge?
558 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
559 my $label = $self->path_display_label( $self->path_witnesses( $edge ) );
560 my $variables = { %edge_attrs, 'label' => $label };
561 # Account for the rank gap if necessary
562 if( $self->reading( $edge->[1] )->has_rank
563 && $self->reading( $edge->[0] )->has_rank
564 && $self->reading( $edge->[1] )->rank
565 - $self->reading( $edge->[0] )->rank > 1 ) {
566 $variables->{'minlen'} = $self->reading( $edge->[1] )->rank
567 - $self->reading( $edge->[0] )->rank;
569 # EXPERIMENTAL: make edge width reflect no. of witnesses
570 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
571 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
573 my $varopts = _dot_attr_string( $variables );
574 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
575 $edge->[0], $edge->[1], $varopts );
576 } elsif( $used{$edge->[0]} ) {
577 $subend{$edge->[0]} = 1;
578 } elsif( $used{$edge->[1]} ) {
579 $substart{$edge->[1]} = 1;
582 # Add substitute start and end edges if necessary
583 foreach my $node ( keys %substart ) {
584 my $witstr = $self->path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
585 my $variables = { %edge_attrs, 'label' => $witstr };
586 my $varopts = _dot_attr_string( $variables );
587 $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
589 foreach my $node ( keys %subend ) {
590 my $witstr = $self->path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
591 my $variables = { %edge_attrs, 'label' => $witstr };
592 my $varopts = _dot_attr_string( $variables );
593 $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
596 if( !$startrank && !$endrank ) {
597 $dot .= "\t\"#END#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
604 sub _dot_attr_string {
607 foreach my $k ( sort keys %$hash ) {
609 push( @attrs, $k.'="'.$v.'"' );
611 return( '[ ' . join( ', ', @attrs ) . ' ]' );
615 my( $self, @edge ) = @_;
616 # If edge is an arrayref, cope.
617 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
621 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
625 sub path_display_label {
628 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
629 if( scalar @wits > $maj ) {
630 # TODO break out a.c. wits
633 return join( ', ', @wits );
640 Returns a GraphML representation of the collation. The GraphML will contain
641 two graphs. The first expresses the attributes of the readings and the witness
642 paths that link them; the second expresses the relationships that link the
643 readings. This is the native transfer format for a tradition.
652 my $datafile = 't/data/florilegium_tei_ps.xml';
653 my $tradition = Text::Tradition->new( 'input' => 'TEI',
658 ok( $tradition, "Got a tradition object" );
659 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
660 ok( $tradition->collation, "Tradition has a collation" );
662 my $c = $tradition->collation;
663 is( scalar $c->readings, $READINGS, "Collation has all readings" );
664 is( scalar $c->paths, $PATHS, "Collation has all paths" );
665 is( scalar $c->relationships, 0, "Collation has all relationships" );
667 # Add a few relationships
668 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
669 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
670 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
672 # Now write it to GraphML and parse it again.
674 my $graphml = $c->as_graphml;
675 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
676 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
677 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
678 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
688 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
689 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
690 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
691 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
693 # Create the document and root node
694 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
695 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
696 $graphml->setDocumentElement( $root );
697 $root->setNamespace( $xsi_ns, 'xsi', 0 );
698 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
700 # Add the data keys for the graph
703 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
704 foreach my $datum ( @graph_attributes ) {
705 $graph_data_keys{$datum} = 'dg'.$gdi++;
706 my $key = $root->addNewChild( $graphml_ns, 'key' );
707 $key->setAttribute( 'attr.name', $datum );
708 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
709 $key->setAttribute( 'for', 'graph' );
710 $key->setAttribute( 'id', $graph_data_keys{$datum} );
713 # Add the data keys for nodes
720 is_start => 'boolean',
722 is_lacuna => 'boolean',
724 foreach my $datum ( keys %node_data ) {
725 $node_data_keys{$datum} = 'dn'.$ndi++;
726 my $key = $root->addNewChild( $graphml_ns, 'key' );
727 $key->setAttribute( 'attr.name', $datum );
728 $key->setAttribute( 'attr.type', $node_data{$datum} );
729 $key->setAttribute( 'for', 'node' );
730 $key->setAttribute( 'id', $node_data_keys{$datum} );
733 # Add the data keys for edges, i.e. witnesses
737 class => 'string', # Class, deprecated soon
738 witness => 'string', # ID/label for a path
739 relationship => 'string', # ID/label for a relationship
740 extra => 'boolean', # Path key
741 scope => 'string', # Relationship key
742 non_correctable => 'boolean', # Relationship key
743 non_independent => 'boolean', # Relationship key
745 foreach my $datum ( keys %edge_data ) {
746 $edge_data_keys{$datum} = 'de'.$edi++;
747 my $key = $root->addNewChild( $graphml_ns, 'key' );
748 $key->setAttribute( 'attr.name', $datum );
749 $key->setAttribute( 'attr.type', $edge_data{$datum} );
750 $key->setAttribute( 'for', 'edge' );
751 $key->setAttribute( 'id', $edge_data_keys{$datum} );
754 # Add the collation graph itself
755 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
756 $sgraph->setAttribute( 'edgedefault', 'directed' );
757 $sgraph->setAttribute( 'id', $self->tradition->name );
758 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
759 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
760 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
761 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
762 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
764 # Collation attribute data
765 foreach my $datum ( @graph_attributes ) {
766 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
767 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
772 # Add our readings to the graph
773 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
774 # Add to the main graph
775 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
776 my $node_xmlid = 'n' . $node_ctr++;
777 $node_hash{ $n->id } = $node_xmlid;
778 $node_el->setAttribute( 'id', $node_xmlid );
779 foreach my $d ( keys %node_data ) {
781 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
786 # Add the path edges to the sequence graph
788 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
789 # We add an edge in the graphml for every witness in $e.
790 foreach my $wit ( sort $self->path_witnesses( $e ) ) {
791 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
792 $node_hash{ $e->[0] },
793 $node_hash{ $e->[1] } );
794 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
795 $edge_el->setAttribute( 'source', $from );
796 $edge_el->setAttribute( 'target', $to );
797 $edge_el->setAttribute( 'id', $id );
799 # It's a witness path, so add the witness
801 my $key = $edge_data_keys{'witness'};
802 # Is this an ante-corr witness?
803 my $aclabel = $self->ac_label;
804 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
805 # Keep the base witness
807 # ...and record that this is an 'extra' reading path
808 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
810 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
811 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
815 # Add the relationship graph to the XML
816 $self->relations->as_graphml( $graphml_ns, $root, \%node_hash,
817 $node_data_keys{'id'}, \%edge_data_keys );
819 # Save and return the thing
820 my $result = decode_utf8( $graphml->toString(1) );
824 sub _add_graphml_data {
825 my( $el, $key, $value ) = @_;
826 return unless defined $value;
827 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
828 $data_el->setAttribute( 'key', $key );
829 $data_el->appendText( $value );
834 Returns a CSV alignment table representation of the collation graph, one
835 row per witness (or witness uncorrected.)
841 my $table = $self->make_alignment_table;
842 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
844 # Make the header row
845 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
846 push( @result, decode_utf8( $csv->string ) );
847 # Make the rest of the rows
848 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
849 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
850 my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
851 $csv->combine( @row );
852 push( @result, decode_utf8( $csv->string ) );
854 return join( "\n", @result );
857 =head2 make_alignment_table( $use_refs, $include_witnesses )
859 Return a reference to an alignment table, in a slightly enhanced CollateX
860 format which looks like this:
862 $table = { alignment => [ { witness => "SIGIL",
863 tokens => [ { t => "TEXT" }, ... ] },
865 tokens => [ { t => "TEXT" }, ... ] },
869 If $use_refs is set to 1, the reading object is returned in the table
870 instead of READINGTEXT; if not, the text of the reading is returned.
872 If $include_witnesses is set to a hashref, only the witnesses whose sigil
873 keys have a true hash value will be included.
877 sub make_alignment_table {
878 my( $self, $noderefs, $include ) = @_;
879 # Make sure we can do this
880 throw( "Need a linear graph in order to make an alignment table" )
881 unless $self->linear;
882 $self->calculate_ranks unless $self->end->has_rank;
884 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
885 my @all_pos = ( 1 .. $self->end->rank - 1 );
886 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
888 next unless $include->{$wit->sigil};
890 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
891 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
892 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
893 push( @{$table->{'alignment'}},
894 { 'witness' => $wit->sigil, 'tokens' => \@row } );
895 if( $wit->is_layered ) {
896 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
897 $wit->sigil.$self->ac_label );
898 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
899 push( @{$table->{'alignment'}},
900 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
906 sub _make_witness_row {
907 my( $path, $positions, $noderefs ) = @_;
909 map { $char_hash{$_} = undef } @$positions;
911 foreach my $rdg ( @$path ) {
912 my $rtext = $rdg->text;
913 $rtext = '#LACUNA#' if $rdg->is_lacuna;
914 print STDERR "rank " . $rdg->rank . "\n" if $debug;
915 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
916 $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
919 my @row = map { $char_hash{$_} } @$positions;
920 # Fill in lacuna markers for undef spots in the row
921 my $last_el = shift @row;
922 my @filled_row = ( $last_el );
923 foreach my $el ( @row ) {
924 # If we are using node reference, make the lacuna node appear many times
925 # in the table. If not, use the lacuna tag.
926 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
927 $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
929 push( @filled_row, $el );
935 # Tiny utility function to say if a table element is a lacuna
938 return 1 if $el->{'t'} eq '#LACUNA#';
939 return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
940 && $el->{'t'}->is_lacuna;
944 # Helper to turn the witnesses along columns rather than rows. Assumes
949 return $result unless scalar @$table;
950 my $nrows = scalar @{$table->[0]};
951 foreach my $idx ( 0 .. $nrows - 1 ) {
952 foreach my $wit ( 0 .. $#{$table} ) {
953 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
959 =head1 NAVIGATION METHODS
961 =head2 reading_sequence( $first, $last, $sigil, $backup )
963 Returns the ordered list of readings, starting with $first and ending
964 with $last, for the witness given in $sigil. If a $backup sigil is
965 specified (e.g. when walking a layered witness), it will be used wherever
966 no $sigil path exists. If there is a base text reading, that will be
967 used wherever no path exists for $sigil or $backup.
971 # TODO Think about returning some lazy-eval iterator.
972 # TODO Get rid of backup; we should know from what witness is whether we need it.
974 sub reading_sequence {
975 my( $self, $start, $end, $witness ) = @_;
977 $witness = $self->baselabel unless $witness;
978 my @readings = ( $start );
981 while( $n && $n->id ne $end->id ) {
982 if( exists( $seen{$n->id} ) ) {
983 throw( "Detected loop for $witness at " . $n->id );
987 my $next = $self->next_reading( $n, $witness );
989 throw( "Did not find any path for $witness from reading " . $n->id );
991 push( @readings, $next );
994 # Check that the last reading is our end reading.
995 my $last = $readings[$#readings];
996 throw( "Last reading found from " . $start->text .
997 " for witness $witness is not the end!" ) # TODO do we get this far?
998 unless $last->id eq $end->id;
1003 =head2 next_reading( $reading, $sigil );
1005 Returns the reading that follows the given reading along the given witness
1011 # Return the successor via the corresponding path.
1013 my $answer = $self->_find_linked_reading( 'next', @_ );
1014 return undef unless $answer;
1015 return $self->reading( $answer );
1018 =head2 prior_reading( $reading, $sigil )
1020 Returns the reading that precedes the given reading along the given witness
1026 # Return the predecessor via the corresponding path.
1028 my $answer = $self->_find_linked_reading( 'prior', @_ );
1029 return $self->reading( $answer );
1032 sub _find_linked_reading {
1033 my( $self, $direction, $node, $path ) = @_;
1035 # Get a backup if we are dealing with a layered witness
1037 my $aclabel = $self->ac_label;
1038 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1042 my @linked_paths = $direction eq 'next'
1043 ? $self->sequence->edges_from( $node )
1044 : $self->sequence->edges_to( $node );
1045 return undef unless scalar( @linked_paths );
1047 # We have to find the linked path that contains all of the
1048 # witnesses supplied in $path.
1049 my( @path_wits, @alt_path_wits );
1050 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1051 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1054 foreach my $le ( @linked_paths ) {
1055 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1058 my @le_wits = sort $self->path_witnesses( $le );
1059 if( _is_within( \@path_wits, \@le_wits ) ) {
1060 # This is the right path.
1061 return $direction eq 'next' ? $le->[1] : $le->[0];
1062 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1066 # Got this far? Return the alternate path if it exists.
1067 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1070 # Got this far? Return the base path if it exists.
1071 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1074 # Got this far? We have no appropriate path.
1075 warn "Could not find $direction node from " . $node->id
1076 . " along path $path";
1082 my( $set1, $set2 ) = @_;
1083 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1084 foreach my $el ( @$set1 ) {
1085 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1090 # Return the string that joins together a list of witnesses for
1091 # display on a single path.
1092 sub _witnesses_of_label {
1093 my( $self, $label ) = @_;
1094 my $regex = $self->wit_list_separator;
1095 my @answer = split( /\Q$regex\E/, $label );
1099 =head2 common_readings
1101 Returns the list of common readings in the graph (i.e. those readings that are
1102 shared by all non-lacunose witnesses.)
1106 sub common_readings {
1108 my @common = grep { $_->is_common } $self->readings;
1112 =head2 path_text( $sigil, $mainsigil [, $start, $end ] )
1114 Returns the text of a witness (plus its backup, if we are using a layer)
1115 as stored in the collation. The text is returned as a string, where the
1116 individual readings are joined with spaces and the meta-readings (e.g.
1117 lacunae) are omitted. Optional specification of $start and $end allows
1118 the generation of a subset of the witness text.
1123 my( $self, $wit, $start, $end ) = @_;
1124 $start = $self->start unless $start;
1125 $end = $self->end unless $end;
1126 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1127 return join( ' ', map { $_->text } @path );
1130 =head1 INITIALIZATION METHODS
1132 These are mostly for use by parsers.
1134 =head2 make_witness_path( $witness )
1136 Link the array of readings contained in $witness->path (and in
1137 $witness->uncorrected_path if it exists) into collation paths.
1138 Clear out the arrays when finished.
1140 =head2 make_witness_paths
1142 Call make_witness_path for all witnesses in the tradition.
1146 # For use when a collation is constructed from a base text and an apparatus.
1147 # We have the sequences of readings and just need to add path edges.
1148 # When we are done, clear out the witness path attributes, as they are no
1150 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1152 sub make_witness_paths {
1154 foreach my $wit ( $self->tradition->witnesses ) {
1155 # print STDERR "Making path for " . $wit->sigil . "\n";
1156 $self->make_witness_path( $wit );
1160 sub make_witness_path {
1161 my( $self, $wit ) = @_;
1162 my @chain = @{$wit->path};
1163 my $sig = $wit->sigil;
1164 foreach my $idx ( 0 .. $#chain-1 ) {
1165 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1167 if( $wit->is_layered ) {
1168 @chain = @{$wit->uncorrected_path};
1169 foreach my $idx( 0 .. $#chain-1 ) {
1170 my $source = $chain[$idx];
1171 my $target = $chain[$idx+1];
1172 $self->add_path( $source, $target, $sig.$self->ac_label )
1173 unless $self->has_path( $source, $target, $sig );
1177 $wit->clear_uncorrected_path;
1180 =head2 calculate_ranks
1182 Calculate the reading ranks (that is, their aligned positions relative
1183 to each other) for the graph. This can only be called on linear collations.
1187 sub calculate_ranks {
1189 # Walk a version of the graph where every node linked by a relationship
1190 # edge is fundamentally the same node, and do a topological ranking on
1191 # the nodes in this graph.
1192 my $topo_graph = Graph->new();
1196 foreach my $r ( $self->readings ) {
1197 next if exists $rel_containers{$r->id};
1198 my @rels = $r->related_readings( 'colocated' );
1200 # Make a relationship container.
1202 my $rn = 'rel_container_' . $rel_ctr++;
1203 $topo_graph->add_vertex( $rn );
1205 $rel_containers{$_->id} = $rn;
1208 # Add a new node to mirror the old node.
1209 $rel_containers{$r->id} = $r->id;
1210 $topo_graph->add_vertex( $r->id );
1215 foreach my $r ( $self->readings ) {
1216 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1217 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1218 $rel_containers{$n} );
1219 # $DB::single = 1 unless $tfrom && $tto;
1220 $topo_graph->add_edge( $tfrom, $tto );
1224 # Now do the rankings, starting with the start node.
1225 my $topo_start = $rel_containers{$self->start->id};
1226 my $node_ranks = { $topo_start => 0 };
1227 my @curr_origin = ( $topo_start );
1228 # A little iterative function.
1229 while( @curr_origin ) {
1230 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1232 # Transfer our rankings from the topological graph to the real one.
1233 foreach my $r ( $self->readings ) {
1234 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1235 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1237 # Die. Find the last rank we calculated.
1238 my @all_defined = sort { $node_ranks->{$rel_containers{$a->id}}
1239 <=> $node_ranks->{$rel_containers{$b->id}} }
1241 my $last = pop @all_defined;
1242 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1248 my( $graph, $node_ranks, @current_nodes ) = @_;
1249 # Look at each of the children of @current_nodes. If all the child's
1250 # parents have a rank, assign it the highest rank + 1 and add it to
1251 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1252 # parent gets a rank.
1254 foreach my $c ( @current_nodes ) {
1255 warn "Current reading $c has no rank!"
1256 unless exists $node_ranks->{$c};
1257 # print STDERR "Looking at child of node $c, rank "
1258 # . $node_ranks->{$c} . "\n";
1259 foreach my $child ( $graph->successors( $c ) ) {
1260 next if exists $node_ranks->{$child};
1261 my $highest_rank = -1;
1263 foreach my $parent ( $graph->predecessors( $child ) ) {
1264 if( exists $node_ranks->{$parent} ) {
1265 $highest_rank = $node_ranks->{$parent}
1266 if $highest_rank <= $node_ranks->{$parent};
1273 my $c_rank = $highest_rank + 1;
1274 # print STDERR "Assigning rank $c_rank to node $child \n";
1275 $node_ranks->{$child} = $c_rank;
1276 push( @next_nodes, $child );
1282 =head2 flatten_ranks
1284 A convenience method for parsing collation data. Searches the graph for readings
1285 with the same text at the same rank, and merges any that are found.
1291 my %unique_rank_rdg;
1292 foreach my $rdg ( $self->readings ) {
1293 next unless $rdg->has_rank;
1294 my $key = $rdg->rank . "||" . $rdg->text;
1295 if( exists $unique_rank_rdg{$key} ) {
1297 # print STDERR "Combining readings at same rank: $key\n";
1298 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1299 # TODO see if this now makes a common point.
1301 $unique_rank_rdg{$key} = $rdg;
1306 =head2 calculate_common_readings
1308 Goes through the graph identifying the readings that appear in every witness
1309 (apart from those with lacunae at that spot.) Marks them as common and returns
1314 use Text::Tradition;
1316 my $cxfile = 't/data/Collatex-16.xml';
1317 my $t = Text::Tradition->new(
1319 'input' => 'CollateX',
1322 my $c = $t->collation;
1324 my @common = $c->calculate_common_readings();
1325 is( scalar @common, 8, "Found correct number of common readings" );
1326 my @marked = sort $c->common_readings();
1327 is( scalar @common, 8, "All common readings got marked as such" );
1328 my @expected = qw/ n1 n12 n16 n19 n20 n5 n6 n7 /;
1329 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1335 sub calculate_common_readings {
1338 my $table = $self->make_alignment_table( 1 );
1339 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1340 my @row = map { $_->{'tokens'}->[$idx]->{'t'} } @{$table->{'alignment'}};
1342 foreach my $r ( @row ) {
1344 $hash{$r->id} = $r unless $r->is_meta;
1346 $hash{'UNDEF'} = $r;
1349 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1350 my( $r ) = values %hash;
1352 push( @common, $r );
1358 =head2 text_from_paths
1360 Calculate the text array for all witnesses from the path, for later consistency
1361 checking. Only to be used if there is no non-graph-based way to know the
1366 sub text_from_paths {
1368 foreach my $wit ( $self->tradition->witnesses ) {
1369 my @text = split( /\s+/,
1370 $self->reading_sequence( $self->start, $self->end, $wit->sigil ) );
1371 $wit->text( \@text );
1372 if( $wit->is_layered ) {
1373 my @uctext = split( /\s+/,
1374 $self->reading_sequence( $self->start, $self->end,
1375 $wit->sigil.$self->ac_label ) );
1376 $wit->text( \@uctext );
1381 =head1 UTILITY FUNCTIONS
1383 =head2 common_predecessor( $reading_a, $reading_b )
1385 Find the last reading that occurs in sequence before both the given readings.
1387 =head2 common_successor( $reading_a, $reading_b )
1389 Find the first reading that occurs in sequence after both the given readings.
1393 use Text::Tradition;
1395 my $cxfile = 't/data/Collatex-16.xml';
1396 my $t = Text::Tradition->new(
1398 'input' => 'CollateX',
1401 my $c = $t->collation;
1403 is( $c->common_predecessor( 'n9', 'n23' )->id,
1404 'n20', "Found correct common predecessor" );
1405 is( $c->common_successor( 'n9', 'n23' )->id,
1406 '#END#', "Found correct common successor" );
1408 is( $c->common_predecessor( 'n19', 'n17' )->id,
1409 'n16', "Found correct common predecessor for readings on same path" );
1410 is( $c->common_successor( 'n21', 'n26' )->id,
1411 '#END#', "Found correct common successor for readings on same path" );
1417 ## Return the closest reading that is a predecessor of both the given readings.
1418 sub common_predecessor {
1420 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1421 return $self->common_in_path( $r1, $r2, 'predecessors' );
1424 sub common_successor {
1426 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1427 return $self->common_in_path( $r1, $r2, 'successors' );
1430 sub common_in_path {
1431 my( $self, $r1, $r2, $dir ) = @_;
1432 my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
1433 $iter = $self->end->rank - $iter if $dir eq 'successors';
1435 my @last_checked = ( $r1, $r2 );
1437 while( !@candidates ) {
1439 foreach my $lc ( @last_checked ) {
1440 foreach my $p ( $lc->$dir ) {
1441 if( $all_seen{$p->id} ) {
1442 push( @candidates, $p );
1444 $all_seen{$p->id} = 1;
1445 push( @new_lc, $p );
1449 @last_checked = @new_lc;
1451 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1452 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1456 Text::Tradition::Error->throw(
1457 'ident' => 'Collation error',
1463 __PACKAGE__->meta->make_immutable;
1469 =item * Get rid of $backup in reading_sequence