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;
17 default => sub { Graph->new() },
25 isa => 'Text::Tradition::Collation::RelationshipStore',
27 relationships => 'relationships',
28 related_readings => 'related_readings',
30 writer => '_set_relations',
35 isa => 'Text::Tradition',
40 isa => 'HashRef[Text::Tradition::Collation::Reading]',
44 _add_reading => 'set',
45 del_reading => 'delete',
46 has_reading => 'exists',
49 default => sub { {} },
52 has 'wit_list_separator' => (
61 default => 'base text',
78 isa => 'Text::Tradition::Collation::Reading',
79 writer => '_set_start',
85 isa => 'Text::Tradition::Collation::Reading',
92 Text::Tradition::Collation - a software model for a text collation
97 my $t = Text::Tradition->new(
98 'name' => 'this is a text',
100 'file' => '/path/to/tei_parallel_seg_file.xml' );
102 my $c = $t->collation;
103 my @readings = $c->readings;
104 my @paths = $c->paths;
105 my @relationships = $c->relationships;
107 my $svg_variant_graph = $t->collation->as_svg();
111 Text::Tradition is a library for representation and analysis of collated
112 texts, particularly medieval ones. The Collation is the central feature of
113 a Tradition, where the text, its sequence of readings, and its relationships
114 between readings are actually kept.
120 The constructor. Takes a hash or hashref of the following arguments:
124 =item * tradition - The Text::Tradition object to which the collation
127 =item * linear - Whether the collation should be linear; that is, whether
128 transposed readings should be treated as two linked readings rather than one,
129 and therefore whether the collation graph is acyclic. Defaults to true.
131 =item * baselabel - The default label for the path taken by a base text
132 (if any). Defaults to 'base text'.
134 =item * wit_list_separator - The string to join a list of witnesses for
135 purposes of making labels in display graphs. Defaults to ', '.
137 =item * ac_label - The extra label to tack onto a witness sigil when
138 representing another layer of path for the given witness - that is, when
139 a text has more than one possible reading due to scribal corrections or
140 the like. Defaults to ' (a.c.)'.
150 =head2 wit_list_separator
156 Simple accessors for collation attributes.
160 The meta-reading at the start of every witness path.
164 The meta-reading at the end of every witness path.
168 Returns all Reading objects in the graph.
170 =head2 reading( $id )
172 Returns the Reading object corresponding to the given ID.
174 =head2 add_reading( $reading_args )
176 Adds a new reading object to the collation.
177 See L<Text::Tradition::Collation::Reading> for the available arguments.
179 =head2 del_reading( $object_or_id )
181 Removes the given reading from the collation, implicitly removing its
182 paths and relationships.
184 =head2 merge_readings( $main, $second )
186 Merges the $second reading into the $main one.
187 The arguments may be either readings or reading IDs.
189 =head2 has_reading( $id )
191 Predicate to see whether a given reading ID is in the graph.
193 =head2 reading_witnesses( $object_or_id )
195 Returns a list of sigils whose witnesses contain the reading.
199 Returns all reading paths within the document - that is, all edges in the
200 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
202 =head2 add_path( $source, $target, $sigil )
204 Links the given readings in the collation in sequence, under the given witness
205 sigil. The readings may be specified by object or ID.
207 =head2 del_path( $source, $target, $sigil )
209 Links the given readings in the collation in sequence, under the given witness
210 sigil. The readings may be specified by object or ID.
212 =head2 has_path( $source, $target );
214 Returns true if the two readings are linked in sequence in any witness.
215 The readings may be specified by object or ID.
219 Returns all Relationship objects in the collation.
221 =head2 add_relationship( $reading, $other_reading, $options )
223 Adds a new relationship of the type given in $options between the two readings,
224 which may be specified by object or ID. Returns a value of ( $status, @vectors)
225 where $status is true on success, and @vectors is a list of relationship edges
226 that were ultimately added.
227 See L<Text::Tradition::Collation::Relationship> for the available options.
233 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
234 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
235 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
238 ### Reading construct/destruct functions
241 my( $self, $reading ) = @_;
242 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
243 my %args = %$reading;
244 $reading = Text::Tradition::Collation::Reading->new(
245 'collation' => $self,
248 # First check to see if a reading with this ID exists.
249 if( $self->reading( $reading->id ) ) {
250 throw( "Collation already has a reading with id " . $reading->id );
252 $self->_add_reading( $reading->id => $reading );
253 # Once the reading has been added, put it in both graphs.
254 $self->sequence->add_vertex( $reading->id );
255 $self->relations->add_reading( $reading->id );
259 around del_reading => sub {
264 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
267 # Remove the reading from the graphs.
268 $self->sequence->delete_vertex( $arg );
269 $self->relations->delete_reading( $arg );
272 $self->$orig( $arg );
275 # merge_readings( $main, $to_be_deleted );
280 # We only need the IDs for adding paths to the graph, not the reading
281 # objects themselves.
282 my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
284 # The kept reading should inherit the paths and the relationships
285 # of the deleted reading.
286 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
287 my @vector = ( $kept );
288 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
289 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
290 next if $vector[0] eq $vector[1]; # Don't add a self loop
291 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
292 $self->sequence->add_edge( @vector );
293 my $fwits = $self->sequence->get_edge_attributes( @vector );
294 @wits{keys %$fwits} = values %$fwits;
295 $self->sequence->set_edge_attributes( @vector, \%wits );
297 $self->relations->merge_readings( $kept, $deleted, $combine_char );
299 # Do the deletion deed.
300 if( $combine_char ) {
301 my $kept_obj = $self->reading( $kept );
302 my $new_text = join( $combine_char, $kept_obj->text,
303 $self->reading( $deleted )->text );
304 $kept_obj->alter_text( $new_text );
306 $self->del_reading( $deleted );
310 # Helper function for manipulating the graph.
311 sub _stringify_args {
312 my( $self, $first, $second, $arg ) = @_;
314 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
315 $second = $second->id
316 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
317 return( $first, $second, $arg );
320 # Helper function for manipulating the graph.
321 sub _objectify_args {
322 my( $self, $first, $second, $arg ) = @_;
323 $first = $self->reading( $first )
324 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
325 $second = $self->reading( $second )
326 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
327 return( $first, $second, $arg );
334 # We only need the IDs for adding paths to the graph, not the reading
335 # objects themselves.
336 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
338 # Connect the readings
339 $self->sequence->add_edge( $source, $target );
340 # Note the witness in question
341 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
347 if( ref( $_[0] ) eq 'ARRAY' ) {
354 # We only need the IDs for adding paths to the graph, not the reading
355 # objects themselves.
356 my( $source, $target, $wit ) = $self->_stringify_args( @args );
358 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
359 $self->sequence->delete_edge_attribute( $source, $target, $wit );
361 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
362 $self->sequence->delete_edge( $source, $target );
367 # Extra graph-alike utility
370 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
371 return undef unless $self->sequence->has_edge( $source, $target );
372 return $self->sequence->has_edge_attribute( $source, $target, $wit );
375 =head2 clear_witness( @sigil_list )
377 Clear the given witnesses out of the collation entirely, removing references
378 to them in paths, and removing readings that belong only to them. Should only
379 be called via $tradition->del_witness.
384 my( $self, @sigils ) = @_;
386 # Clear the witness(es) out of the paths
387 foreach my $e ( $self->paths ) {
388 foreach my $sig ( @sigils ) {
389 $self->del_path( $e, $sig );
393 # Clear out the newly unused readings
394 foreach my $r ( $self->readings ) {
395 unless( $self->reading_witnesses( $r ) ) {
396 $self->del_reading( $r );
401 sub add_relationship {
403 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
404 my( @vectors ) = $self->relations->add_relationship( $source,
405 $self->reading( $source ), $target, $self->reading( $target ), $opts );
406 # Force a full rank recalculation every time. Yuck.
407 $self->calculate_ranks() if $self->end->has_rank;
411 =head2 reading_witnesses( $reading )
413 Return a list of sigils corresponding to the witnesses in which the reading appears.
417 sub reading_witnesses {
418 my( $self, $reading ) = @_;
419 # We need only check either the incoming or the outgoing edges; I have
420 # arbitrarily chosen "incoming". Thus, special-case the start node.
421 if( $reading eq $self->start ) {
422 return map { $_->sigil } $self->tradition->witnesses;
425 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
426 my $wits = $self->sequence->get_edge_attributes( @$e );
427 @all_witnesses{ keys %$wits } = 1;
429 return keys %all_witnesses;
432 =head1 OUTPUT METHODS
436 Returns an SVG string that represents the graph, via as_dot and graphviz.
443 my @cmd = qw/dot -Tsvg/;
445 my $dotfile = File::Temp->new();
447 # $dotfile->unlink_on_destroy(0);
448 binmode $dotfile, ':utf8';
449 print $dotfile $self->as_dot();
450 push( @cmd, $dotfile->filename );
451 run( \@cmd, ">", binary(), \$svg );
452 $svg = decode_utf8( $svg );
456 =head2 svg_subgraph( $from, $to )
458 Returns an SVG string that represents the portion of the graph given by the
459 specified range. The $from and $to variables refer to ranks within the graph.
464 my( $self, $from, $to ) = @_;
466 my $dot = $self->as_dot( $from, $to );
468 throw( "Could not output a graph with range $from - $to" );
471 my @cmd = qw/dot -Tsvg/;
473 my $dotfile = File::Temp->new();
475 # $dotfile->unlink_on_destroy(0);
476 binmode $dotfile, ':utf8';
478 push( @cmd, $dotfile->filename );
479 run( \@cmd, ">", binary(), \$svg );
480 $svg = decode_utf8( $svg );
485 =head2 as_dot( $from, $to )
487 Returns a string that is the collation graph expressed in dot
488 (i.e. GraphViz) format. If $from or $to is passed, as_dot creates
489 a subgraph rather than the entire graph.
494 my( $self, $startrank, $endrank ) = @_;
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 # TODO consider making some of these things configurable
507 my $graph_name = $self->tradition->name;
508 $graph_name =~ s/[^\w\s]//g;
509 $graph_name = join( '_', split( /\s+/, $graph_name ) );
517 'fillcolor' => 'white',
522 'arrowhead' => 'open',
523 'color' => '#000000',
524 'fontcolor' => '#000000',
527 my $dot = sprintf( "digraph %s {\n", $graph_name );
528 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
529 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
531 # Output substitute start/end readings if necessary
533 $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
536 $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
538 my %used; # Keep track of the readings that actually appear in the graph
539 foreach my $reading ( $self->readings ) {
540 # Only output readings within our rank range.
541 next if $startrank && $reading->rank < $startrank;
542 next if $endrank && $reading->rank > $endrank;
543 $used{$reading->id} = 1;
544 # Need not output nodes without separate labels
545 next if $reading->id eq $reading->text;
547 my $label = $reading->text;
548 $label =~ s/\"/\\\"/g;
549 $rattrs->{'label'} = $label;
550 # TODO make this an option?
551 # $rattrs->{'fillcolor'} = 'green' if $reading->is_common;
552 $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
556 my @edges = $self->paths;
557 my( %substart, %subend );
558 foreach my $edge ( @edges ) {
559 # Do we need to output this edge?
560 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
561 my $label = $self->path_display_label( $self->path_witnesses( $edge ) );
562 my $variables = { %edge_attrs, 'label' => $label };
563 # Account for the rank gap if necessary
564 if( $self->reading( $edge->[1] )->has_rank
565 && $self->reading( $edge->[0] )->has_rank
566 && $self->reading( $edge->[1] )->rank
567 - $self->reading( $edge->[0] )->rank > 1 ) {
568 $variables->{'minlen'} = $self->reading( $edge->[1] )->rank
569 - $self->reading( $edge->[0] )->rank;
571 # EXPERIMENTAL: make edge width reflect no. of witnesses
572 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
573 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
575 my $varopts = _dot_attr_string( $variables );
576 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
577 $edge->[0], $edge->[1], $varopts );
578 } elsif( $used{$edge->[0]} ) {
579 $subend{$edge->[0]} = 1;
580 } elsif( $used{$edge->[1]} ) {
581 $substart{$edge->[1]} = 1;
584 # Add substitute start and end edges if necessary
585 foreach my $node ( keys %substart ) {
586 my $witstr = $self->path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
587 my $variables = { %edge_attrs, 'label' => $witstr };
588 my $varopts = _dot_attr_string( $variables );
589 $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
591 foreach my $node ( keys %subend ) {
592 my $witstr = $self->path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
593 my $variables = { %edge_attrs, 'label' => $witstr };
594 my $varopts = _dot_attr_string( $variables );
595 $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
602 sub _dot_attr_string {
605 foreach my $k ( sort keys %$hash ) {
607 push( @attrs, $k.'="'.$v.'"' );
609 return( '[ ' . join( ', ', @attrs ) . ' ]' );
613 my( $self, @edge ) = @_;
614 # If edge is an arrayref, cope.
615 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
619 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
623 sub path_display_label {
626 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
627 if( scalar @wits > $maj ) {
628 # TODO break out a.c. wits
631 return join( ', ', @wits );
638 Returns a GraphML representation of the collation. The GraphML will contain
639 two graphs. The first expresses the attributes of the readings and the witness
640 paths that link them; the second expresses the relationships that link the
641 readings. This is the native transfer format for a tradition.
650 my $datafile = 't/data/florilegium_tei_ps.xml';
651 my $tradition = Text::Tradition->new( 'input' => 'TEI',
656 ok( $tradition, "Got a tradition object" );
657 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
658 ok( $tradition->collation, "Tradition has a collation" );
660 my $c = $tradition->collation;
661 is( scalar $c->readings, $READINGS, "Collation has all readings" );
662 is( scalar $c->paths, $PATHS, "Collation has all paths" );
663 is( scalar $c->relationships, 0, "Collation has all relationships" );
665 # Add a few relationships
666 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
667 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
668 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
670 # Now write it to GraphML and parse it again.
672 my $graphml = $c->as_graphml;
673 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
674 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
675 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
676 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
686 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
687 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
688 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
689 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
691 # Create the document and root node
692 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
693 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
694 $graphml->setDocumentElement( $root );
695 $root->setNamespace( $xsi_ns, 'xsi', 0 );
696 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
698 # Add the data keys for the graph
701 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
702 foreach my $datum ( @graph_attributes ) {
703 $graph_data_keys{$datum} = 'dg'.$gdi++;
704 my $key = $root->addNewChild( $graphml_ns, 'key' );
705 $key->setAttribute( 'attr.name', $datum );
706 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
707 $key->setAttribute( 'for', 'graph' );
708 $key->setAttribute( 'id', $graph_data_keys{$datum} );
711 # Add the data keys for nodes
718 is_start => 'boolean',
720 is_lacuna => 'boolean',
722 foreach my $datum ( keys %node_data ) {
723 $node_data_keys{$datum} = 'dn'.$ndi++;
724 my $key = $root->addNewChild( $graphml_ns, 'key' );
725 $key->setAttribute( 'attr.name', $datum );
726 $key->setAttribute( 'attr.type', $node_data{$datum} );
727 $key->setAttribute( 'for', 'node' );
728 $key->setAttribute( 'id', $node_data_keys{$datum} );
731 # Add the data keys for edges, i.e. witnesses
735 class => 'string', # Class, deprecated soon
736 witness => 'string', # ID/label for a path
737 relationship => 'string', # ID/label for a relationship
738 extra => 'boolean', # Path key
739 scope => 'string', # Relationship key
740 non_correctable => 'boolean', # Relationship key
741 non_independent => 'boolean', # Relationship key
743 foreach my $datum ( keys %edge_data ) {
744 $edge_data_keys{$datum} = 'de'.$edi++;
745 my $key = $root->addNewChild( $graphml_ns, 'key' );
746 $key->setAttribute( 'attr.name', $datum );
747 $key->setAttribute( 'attr.type', $edge_data{$datum} );
748 $key->setAttribute( 'for', 'edge' );
749 $key->setAttribute( 'id', $edge_data_keys{$datum} );
752 # Add the collation graph itself
753 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
754 $sgraph->setAttribute( 'edgedefault', 'directed' );
755 $sgraph->setAttribute( 'id', $self->tradition->name );
756 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
757 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
758 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
759 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
760 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
762 # Collation attribute data
763 foreach my $datum ( @graph_attributes ) {
764 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
765 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
770 # Add our readings to the graph
771 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
772 # Add to the main graph
773 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
774 my $node_xmlid = 'n' . $node_ctr++;
775 $node_hash{ $n->id } = $node_xmlid;
776 $node_el->setAttribute( 'id', $node_xmlid );
777 foreach my $d ( keys %node_data ) {
779 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
784 # Add the path edges to the sequence graph
786 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
787 # We add an edge in the graphml for every witness in $e.
788 foreach my $wit ( sort $self->path_witnesses( $e ) ) {
789 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
790 $node_hash{ $e->[0] },
791 $node_hash{ $e->[1] } );
792 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
793 $edge_el->setAttribute( 'source', $from );
794 $edge_el->setAttribute( 'target', $to );
795 $edge_el->setAttribute( 'id', $id );
797 # It's a witness path, so add the witness
799 my $key = $edge_data_keys{'witness'};
800 # Is this an ante-corr witness?
801 my $aclabel = $self->ac_label;
802 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
803 # Keep the base witness
805 # ...and record that this is an 'extra' reading path
806 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
808 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
809 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
813 # Add the relationship graph to the XML
814 $self->relations->as_graphml( $graphml_ns, $root, \%node_hash,
815 $node_data_keys{'id'}, \%edge_data_keys );
817 # Save and return the thing
818 my $result = decode_utf8( $graphml->toString(1) );
822 sub _add_graphml_data {
823 my( $el, $key, $value ) = @_;
824 return unless defined $value;
825 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
826 $data_el->setAttribute( 'key', $key );
827 $data_el->appendText( $value );
832 Returns a CSV alignment table representation of the collation graph, one
833 row per witness (or witness uncorrected.)
839 my $table = $self->make_alignment_table;
840 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
842 # Make the header row
843 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
844 push( @result, decode_utf8( $csv->string ) );
845 # Make the rest of the rows
846 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
847 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
848 my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
849 $csv->combine( @row );
850 push( @result, decode_utf8( $csv->string ) );
852 return join( "\n", @result );
855 =head2 make_alignment_table( $use_refs, $include_witnesses )
857 Return a reference to an alignment table, in a slightly enhanced CollateX
858 format which looks like this:
860 $table = { alignment => [ { witness => "SIGIL",
861 tokens => [ { t => "TEXT" }, ... ] },
863 tokens => [ { t => "TEXT" }, ... ] },
867 If $use_refs is set to 1, the reading object is returned in the table
868 instead of READINGTEXT; if not, the text of the reading is returned.
870 If $include_witnesses is set to a hashref, only the witnesses whose sigil
871 keys have a true hash value will be included.
875 sub make_alignment_table {
876 my( $self, $noderefs, $include ) = @_;
877 unless( $self->linear ) {
878 throw( "Need a linear graph in order to make an alignment table" );
880 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
881 my @all_pos = ( 1 .. $self->end->rank - 1 );
882 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
884 next unless $include->{$wit->sigil};
886 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
887 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
888 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
889 push( @{$table->{'alignment'}},
890 { 'witness' => $wit->sigil, 'tokens' => \@row } );
891 if( $wit->is_layered ) {
892 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
893 $wit->sigil.$self->ac_label );
894 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
895 push( @{$table->{'alignment'}},
896 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
902 sub _make_witness_row {
903 my( $path, $positions, $noderefs ) = @_;
905 map { $char_hash{$_} = undef } @$positions;
907 foreach my $rdg ( @$path ) {
908 my $rtext = $rdg->text;
909 $rtext = '#LACUNA#' if $rdg->is_lacuna;
910 print STDERR "rank " . $rdg->rank . "\n" if $debug;
911 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
912 $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
915 my @row = map { $char_hash{$_} } @$positions;
916 # Fill in lacuna markers for undef spots in the row
917 my $last_el = shift @row;
918 my @filled_row = ( $last_el );
919 foreach my $el ( @row ) {
920 # If we are using node reference, make the lacuna node appear many times
921 # in the table. If not, use the lacuna tag.
922 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
923 $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
925 push( @filled_row, $el );
931 # Tiny utility function to say if a table element is a lacuna
934 return 1 if $el->{'t'} eq '#LACUNA#';
935 return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
936 && $el->{'t'}->is_lacuna;
940 # Helper to turn the witnesses along columns rather than rows. Assumes
945 return $result unless scalar @$table;
946 my $nrows = scalar @{$table->[0]};
947 foreach my $idx ( 0 .. $nrows - 1 ) {
948 foreach my $wit ( 0 .. $#{$table} ) {
949 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
955 =head1 NAVIGATION METHODS
957 =head2 reading_sequence( $first, $last, $sigil, $backup )
959 Returns the ordered list of readings, starting with $first and ending
960 with $last, for the witness given in $sigil. If a $backup sigil is
961 specified (e.g. when walking a layered witness), it will be used wherever
962 no $sigil path exists. If there is a base text reading, that will be
963 used wherever no path exists for $sigil or $backup.
967 # TODO Think about returning some lazy-eval iterator.
968 # TODO Get rid of backup; we should know from what witness is whether we need it.
970 sub reading_sequence {
971 my( $self, $start, $end, $witness ) = @_;
973 $witness = $self->baselabel unless $witness;
974 my @readings = ( $start );
977 while( $n && $n->id ne $end->id ) {
978 if( exists( $seen{$n->id} ) ) {
979 throw( "Detected loop for $witness at " . $n->id );
983 my $next = $self->next_reading( $n, $witness );
985 throw( "Did not find any path for $witness from reading " . $n->id );
987 push( @readings, $next );
990 # Check that the last reading is our end reading.
991 my $last = $readings[$#readings];
992 throw( "Last reading found from " . $start->text .
993 " for witness $witness is not the end!" ) # TODO do we get this far?
994 unless $last->id eq $end->id;
999 =head2 next_reading( $reading, $sigil );
1001 Returns the reading that follows the given reading along the given witness
1007 # Return the successor via the corresponding path.
1009 my $answer = $self->_find_linked_reading( 'next', @_ );
1010 return undef unless $answer;
1011 return $self->reading( $answer );
1014 =head2 prior_reading( $reading, $sigil )
1016 Returns the reading that precedes the given reading along the given witness
1022 # Return the predecessor via the corresponding path.
1024 my $answer = $self->_find_linked_reading( 'prior', @_ );
1025 return $self->reading( $answer );
1028 sub _find_linked_reading {
1029 my( $self, $direction, $node, $path ) = @_;
1031 # Get a backup if we are dealing with a layered witness
1033 my $aclabel = $self->ac_label;
1034 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1038 my @linked_paths = $direction eq 'next'
1039 ? $self->sequence->edges_from( $node )
1040 : $self->sequence->edges_to( $node );
1041 return undef unless scalar( @linked_paths );
1043 # We have to find the linked path that contains all of the
1044 # witnesses supplied in $path.
1045 my( @path_wits, @alt_path_wits );
1046 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1047 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1050 foreach my $le ( @linked_paths ) {
1051 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1054 my @le_wits = sort $self->path_witnesses( $le );
1055 if( _is_within( \@path_wits, \@le_wits ) ) {
1056 # This is the right path.
1057 return $direction eq 'next' ? $le->[1] : $le->[0];
1058 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1062 # Got this far? Return the alternate path if it exists.
1063 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1066 # Got this far? Return the base path if it exists.
1067 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1070 # Got this far? We have no appropriate path.
1071 warn "Could not find $direction node from " . $node->id
1072 . " along path $path";
1078 my( $set1, $set2 ) = @_;
1079 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1080 foreach my $el ( @$set1 ) {
1081 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1086 # Return the string that joins together a list of witnesses for
1087 # display on a single path.
1088 sub _witnesses_of_label {
1089 my( $self, $label ) = @_;
1090 my $regex = $self->wit_list_separator;
1091 my @answer = split( /\Q$regex\E/, $label );
1095 =head2 common_readings
1097 Returns the list of common readings in the graph (i.e. those readings that are
1098 shared by all non-lacunose witnesses.)
1102 sub common_readings {
1104 my @common = grep { $_->is_common } $self->readings;
1108 =head2 path_text( $sigil, $mainsigil [, $start, $end ] )
1110 Returns the text of a witness (plus its backup, if we are using a layer)
1111 as stored in the collation. The text is returned as a string, where the
1112 individual readings are joined with spaces and the meta-readings (e.g.
1113 lacunae) are omitted. Optional specification of $start and $end allows
1114 the generation of a subset of the witness text.
1119 my( $self, $wit, $start, $end ) = @_;
1120 $start = $self->start unless $start;
1121 $end = $self->end unless $end;
1122 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1123 return join( ' ', map { $_->text } @path );
1126 =head1 INITIALIZATION METHODS
1128 These are mostly for use by parsers.
1130 =head2 make_witness_path( $witness )
1132 Link the array of readings contained in $witness->path (and in
1133 $witness->uncorrected_path if it exists) into collation paths.
1134 Clear out the arrays when finished.
1136 =head2 make_witness_paths
1138 Call make_witness_path for all witnesses in the tradition.
1142 # For use when a collation is constructed from a base text and an apparatus.
1143 # We have the sequences of readings and just need to add path edges.
1144 # When we are done, clear out the witness path attributes, as they are no
1146 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1148 sub make_witness_paths {
1150 foreach my $wit ( $self->tradition->witnesses ) {
1151 # print STDERR "Making path for " . $wit->sigil . "\n";
1152 $self->make_witness_path( $wit );
1156 sub make_witness_path {
1157 my( $self, $wit ) = @_;
1158 my @chain = @{$wit->path};
1159 my $sig = $wit->sigil;
1160 foreach my $idx ( 0 .. $#chain-1 ) {
1161 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1163 if( $wit->is_layered ) {
1164 @chain = @{$wit->uncorrected_path};
1165 foreach my $idx( 0 .. $#chain-1 ) {
1166 my $source = $chain[$idx];
1167 my $target = $chain[$idx+1];
1168 $self->add_path( $source, $target, $sig.$self->ac_label )
1169 unless $self->has_path( $source, $target, $sig );
1173 $wit->clear_uncorrected_path;
1176 =head2 calculate_ranks
1178 Calculate the reading ranks (that is, their aligned positions relative
1179 to each other) for the graph. This can only be called on linear collations.
1183 sub calculate_ranks {
1185 # Walk a version of the graph where every node linked by a relationship
1186 # edge is fundamentally the same node, and do a topological ranking on
1187 # the nodes in this graph.
1188 my $topo_graph = Graph->new();
1192 foreach my $r ( $self->readings ) {
1193 next if exists $rel_containers{$r->id};
1194 my @rels = $r->related_readings( 'colocated' );
1196 # Make a relationship container.
1198 my $rn = 'rel_container_' . $rel_ctr++;
1199 $topo_graph->add_vertex( $rn );
1201 $rel_containers{$_->id} = $rn;
1204 # Add a new node to mirror the old node.
1205 $rel_containers{$r->id} = $r->id;
1206 $topo_graph->add_vertex( $r->id );
1211 foreach my $r ( $self->readings ) {
1212 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1213 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1214 $rel_containers{$n} );
1215 # $DB::single = 1 unless $tfrom && $tto;
1216 $topo_graph->add_edge( $tfrom, $tto );
1220 # Now do the rankings, starting with the start node.
1221 my $topo_start = $rel_containers{$self->start->id};
1222 my $node_ranks = { $topo_start => 0 };
1223 my @curr_origin = ( $topo_start );
1224 # A little iterative function.
1225 while( @curr_origin ) {
1226 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1228 # Transfer our rankings from the topological graph to the real one.
1229 foreach my $r ( $self->readings ) {
1230 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1231 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1233 # Die. Find the last rank we calculated.
1234 my @all_defined = sort { $node_ranks->{$rel_containers{$a->id}}
1235 <=> $node_ranks->{$rel_containers{$b->id}} }
1237 my $last = pop @all_defined;
1238 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1244 my( $graph, $node_ranks, @current_nodes ) = @_;
1245 # Look at each of the children of @current_nodes. If all the child's
1246 # parents have a rank, assign it the highest rank + 1 and add it to
1247 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1248 # parent gets a rank.
1250 foreach my $c ( @current_nodes ) {
1251 warn "Current reading $c has no rank!"
1252 unless exists $node_ranks->{$c};
1253 # print STDERR "Looking at child of node $c, rank "
1254 # . $node_ranks->{$c} . "\n";
1255 foreach my $child ( $graph->successors( $c ) ) {
1256 next if exists $node_ranks->{$child};
1257 my $highest_rank = -1;
1259 foreach my $parent ( $graph->predecessors( $child ) ) {
1260 if( exists $node_ranks->{$parent} ) {
1261 $highest_rank = $node_ranks->{$parent}
1262 if $highest_rank <= $node_ranks->{$parent};
1269 my $c_rank = $highest_rank + 1;
1270 # print STDERR "Assigning rank $c_rank to node $child \n";
1271 $node_ranks->{$child} = $c_rank;
1272 push( @next_nodes, $child );
1278 =head2 flatten_ranks
1280 A convenience method for parsing collation data. Searches the graph for readings
1281 with the same text at the same rank, and merges any that are found.
1287 my %unique_rank_rdg;
1288 foreach my $rdg ( $self->readings ) {
1289 next unless $rdg->has_rank;
1290 my $key = $rdg->rank . "||" . $rdg->text;
1291 if( exists $unique_rank_rdg{$key} ) {
1293 # print STDERR "Combining readings at same rank: $key\n";
1294 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1296 $unique_rank_rdg{$key} = $rdg;
1301 =head2 calculate_common_readings
1303 Goes through the graph identifying the readings that appear in every witness
1304 (apart from those with lacunae at that spot.) Marks them as common and returns
1309 use Text::Tradition;
1311 my $cxfile = 't/data/Collatex-16.xml';
1312 my $t = Text::Tradition->new(
1314 'input' => 'CollateX',
1317 my $c = $t->collation;
1319 my @common = $c->calculate_common_readings();
1320 is( scalar @common, 8, "Found correct number of common readings" );
1321 my @marked = sort $c->common_readings();
1322 is( scalar @common, 8, "All common readings got marked as such" );
1323 my @expected = qw/ n1 n12 n16 n19 n20 n5 n6 n7 /;
1324 is_deeply( \@marked, \@expected, "Found correct list of common readings" );
1330 sub calculate_common_readings {
1333 my $table = $self->make_alignment_table( 1 );
1334 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
1335 my @row = map { $_->{'tokens'}->[$idx]->{'t'} } @{$table->{'alignment'}};
1337 foreach my $r ( @row ) {
1339 $hash{$r->id} = $r unless $r->is_meta;
1341 $hash{'UNDEF'} = $r;
1344 if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
1345 my( $r ) = values %hash;
1347 push( @common, $r );
1353 =head2 text_from_paths
1355 Calculate the text array for all witnesses from the path, for later consistency
1356 checking. Only to be used if there is no non-graph-based way to know the
1361 sub text_from_paths {
1363 foreach my $wit ( $self->tradition->witnesses ) {
1364 my @text = split( /\s+/,
1365 $self->reading_sequence( $self->start, $self->end, $wit->sigil ) );
1366 $wit->text( \@text );
1367 if( $wit->is_layered ) {
1368 my @uctext = split( /\s+/,
1369 $self->reading_sequence( $self->start, $self->end,
1370 $wit->sigil.$self->ac_label ) );
1371 $wit->text( \@uctext );
1376 =head1 UTILITY FUNCTIONS
1378 =head2 common_predecessor( $reading_a, $reading_b )
1380 Find the last reading that occurs in sequence before both the given readings.
1382 =head2 common_successor( $reading_a, $reading_b )
1384 Find the first reading that occurs in sequence after both the given readings.
1388 use Text::Tradition;
1390 my $cxfile = 't/data/Collatex-16.xml';
1391 my $t = Text::Tradition->new(
1393 'input' => 'CollateX',
1396 my $c = $t->collation;
1398 is( $c->common_predecessor( 'n9', 'n23' )->id,
1399 'n20', "Found correct common predecessor" );
1400 is( $c->common_successor( 'n9', 'n23' )->id,
1401 '#END#', "Found correct common successor" );
1403 is( $c->common_predecessor( 'n19', 'n17' )->id,
1404 'n16', "Found correct common predecessor for readings on same path" );
1405 is( $c->common_successor( 'n21', 'n26' )->id,
1406 '#END#', "Found correct common successor for readings on same path" );
1412 ## Return the closest reading that is a predecessor of both the given readings.
1413 sub common_predecessor {
1415 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1416 return $self->common_in_path( $r1, $r2, 'predecessors' );
1419 sub common_successor {
1421 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1422 return $self->common_in_path( $r1, $r2, 'successors' );
1425 sub common_in_path {
1426 my( $self, $r1, $r2, $dir ) = @_;
1427 my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
1428 $iter = $self->end->rank - $iter if $dir eq 'successors';
1430 my @last_checked = ( $r1, $r2 );
1432 while( !@candidates ) {
1434 foreach my $lc ( @last_checked ) {
1435 foreach my $p ( $lc->$dir ) {
1436 if( $all_seen{$p->id} ) {
1437 push( @candidates, $p );
1439 $all_seen{$p->id} = 1;
1440 push( @new_lc, $p );
1444 @last_checked = @new_lc;
1446 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1447 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1451 Text::Tradition::Error->throw(
1452 'ident' => 'Collation error',
1458 __PACKAGE__->meta->make_immutable;
1464 =item * Get rid of $backup in reading_sequence