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;
546 my $label = $reading->text;
547 $label =~ s/\"/\\\"/g;
548 $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
552 my @edges = $self->paths;
553 my( %substart, %subend );
554 foreach my $edge ( @edges ) {
555 # Do we need to output this edge?
556 if( $used{$edge->[0]} && $used{$edge->[1]} ) {
557 my $label = $self->path_display_label( $self->path_witnesses( $edge ) );
558 my $variables = { %edge_attrs, 'label' => $label };
559 # Account for the rank gap if necessary
560 if( $self->reading( $edge->[1] )->has_rank
561 && $self->reading( $edge->[0] )->has_rank
562 && $self->reading( $edge->[1] )->rank
563 - $self->reading( $edge->[0] )->rank > 1 ) {
564 $variables->{'minlen'} = $self->reading( $edge->[1] )->rank
565 - $self->reading( $edge->[0] )->rank;
567 # EXPERIMENTAL: make edge width reflect no. of witnesses
568 my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
569 $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
571 my $varopts = _dot_attr_string( $variables );
572 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
573 $edge->[0], $edge->[1], $varopts );
574 } elsif( $used{$edge->[0]} ) {
575 $subend{$edge->[0]} = 1;
576 } elsif( $used{$edge->[1]} ) {
577 $substart{$edge->[1]} = 1;
580 # Add substitute start and end edges if necessary
581 foreach my $node ( keys %substart ) {
582 my $witstr = $self->path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
583 my $variables = { %edge_attrs, 'label' => $witstr };
584 my $varopts = _dot_attr_string( $variables );
585 $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
587 foreach my $node ( keys %subend ) {
588 my $witstr = $self->path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
589 my $variables = { %edge_attrs, 'label' => $witstr };
590 my $varopts = _dot_attr_string( $variables );
591 $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
598 sub _dot_attr_string {
601 foreach my $k ( sort keys %$hash ) {
603 push( @attrs, $k.'="'.$v.'"' );
605 return( '[ ' . join( ', ', @attrs ) . ' ]' );
609 my( $self, @edge ) = @_;
610 # If edge is an arrayref, cope.
611 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
615 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
619 sub path_display_label {
622 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
623 if( scalar @wits > $maj ) {
624 # TODO break out a.c. wits
627 return join( ', ', @wits );
634 Returns a GraphML representation of the collation. The GraphML will contain
635 two graphs. The first expresses the attributes of the readings and the witness
636 paths that link them; the second expresses the relationships that link the
637 readings. This is the native transfer format for a tradition.
646 my $datafile = 't/data/florilegium_tei_ps.xml';
647 my $tradition = Text::Tradition->new( 'input' => 'TEI',
652 ok( $tradition, "Got a tradition object" );
653 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
654 ok( $tradition->collation, "Tradition has a collation" );
656 my $c = $tradition->collation;
657 is( scalar $c->readings, $READINGS, "Collation has all readings" );
658 is( scalar $c->paths, $PATHS, "Collation has all paths" );
659 is( scalar $c->relationships, 0, "Collation has all relationships" );
661 # Add a few relationships
662 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
663 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
664 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
666 # Now write it to GraphML and parse it again.
668 my $graphml = $c->as_graphml;
669 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
670 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
671 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
672 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
682 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
683 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
684 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
685 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
687 # Create the document and root node
688 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
689 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
690 $graphml->setDocumentElement( $root );
691 $root->setNamespace( $xsi_ns, 'xsi', 0 );
692 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
694 # Add the data keys for the graph
697 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
698 foreach my $datum ( @graph_attributes ) {
699 $graph_data_keys{$datum} = 'dg'.$gdi++;
700 my $key = $root->addNewChild( $graphml_ns, 'key' );
701 $key->setAttribute( 'attr.name', $datum );
702 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
703 $key->setAttribute( 'for', 'graph' );
704 $key->setAttribute( 'id', $graph_data_keys{$datum} );
707 # Add the data keys for nodes
714 is_start => 'boolean',
716 is_lacuna => 'boolean',
718 foreach my $datum ( keys %node_data ) {
719 $node_data_keys{$datum} = 'dn'.$ndi++;
720 my $key = $root->addNewChild( $graphml_ns, 'key' );
721 $key->setAttribute( 'attr.name', $datum );
722 $key->setAttribute( 'attr.type', $node_data{$datum} );
723 $key->setAttribute( 'for', 'node' );
724 $key->setAttribute( 'id', $node_data_keys{$datum} );
727 # Add the data keys for edges, i.e. witnesses
731 class => 'string', # Class, deprecated soon
732 witness => 'string', # ID/label for a path
733 relationship => 'string', # ID/label for a relationship
734 extra => 'boolean', # Path key
735 scope => 'string', # Relationship key
736 non_correctable => 'boolean', # Relationship key
737 non_independent => 'boolean', # Relationship key
739 foreach my $datum ( keys %edge_data ) {
740 $edge_data_keys{$datum} = 'de'.$edi++;
741 my $key = $root->addNewChild( $graphml_ns, 'key' );
742 $key->setAttribute( 'attr.name', $datum );
743 $key->setAttribute( 'attr.type', $edge_data{$datum} );
744 $key->setAttribute( 'for', 'edge' );
745 $key->setAttribute( 'id', $edge_data_keys{$datum} );
748 # Add the collation graph itself
749 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
750 $sgraph->setAttribute( 'edgedefault', 'directed' );
751 $sgraph->setAttribute( 'id', $self->tradition->name );
752 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
753 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
754 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
755 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
756 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
758 # Collation attribute data
759 foreach my $datum ( @graph_attributes ) {
760 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
761 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
766 # Add our readings to the graph
767 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
768 # Add to the main graph
769 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
770 my $node_xmlid = 'n' . $node_ctr++;
771 $node_hash{ $n->id } = $node_xmlid;
772 $node_el->setAttribute( 'id', $node_xmlid );
773 foreach my $d ( keys %node_data ) {
775 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
780 # Add the path edges to the sequence graph
782 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
783 # We add an edge in the graphml for every witness in $e.
784 foreach my $wit ( sort $self->path_witnesses( $e ) ) {
785 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
786 $node_hash{ $e->[0] },
787 $node_hash{ $e->[1] } );
788 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
789 $edge_el->setAttribute( 'source', $from );
790 $edge_el->setAttribute( 'target', $to );
791 $edge_el->setAttribute( 'id', $id );
793 # It's a witness path, so add the witness
795 my $key = $edge_data_keys{'witness'};
796 # Is this an ante-corr witness?
797 my $aclabel = $self->ac_label;
798 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
799 # Keep the base witness
801 # ...and record that this is an 'extra' reading path
802 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
804 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
805 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
809 # Add the relationship graph to the XML
810 $self->relations->as_graphml( $graphml_ns, $root, \%node_hash,
811 $node_data_keys{'id'}, \%edge_data_keys );
813 # Save and return the thing
814 my $result = decode_utf8( $graphml->toString(1) );
818 sub _add_graphml_data {
819 my( $el, $key, $value ) = @_;
820 return unless defined $value;
821 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
822 $data_el->setAttribute( 'key', $key );
823 $data_el->appendText( $value );
828 Returns a CSV alignment table representation of the collation graph, one
829 row per witness (or witness uncorrected.)
835 my $table = $self->make_alignment_table;
836 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
838 # Make the header row
839 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
840 push( @result, decode_utf8( $csv->string ) );
841 # Make the rest of the rows
842 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
843 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
844 my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
845 $csv->combine( @row );
846 push( @result, decode_utf8( $csv->string ) );
848 return join( "\n", @result );
851 =head2 make_alignment_table( $use_refs, $include_witnesses )
853 Return a reference to an alignment table, in a slightly enhanced CollateX
854 format which looks like this:
856 $table = { alignment => [ { witness => "SIGIL",
857 tokens => [ { t => "TEXT" }, ... ] },
859 tokens => [ { t => "TEXT" }, ... ] },
863 If $use_refs is set to 1, the reading object is returned in the table
864 instead of READINGTEXT; if not, the text of the reading is returned.
866 If $include_witnesses is set to a hashref, only the witnesses whose sigil
867 keys have a true hash value will be included.
871 sub make_alignment_table {
872 my( $self, $noderefs, $include ) = @_;
873 unless( $self->linear ) {
874 throw( "Need a linear graph in order to make an alignment table" );
876 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
877 my @all_pos = ( 1 .. $self->end->rank - 1 );
878 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
880 next unless $include->{$wit->sigil};
882 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
883 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
884 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
885 push( @{$table->{'alignment'}},
886 { 'witness' => $wit->sigil, 'tokens' => \@row } );
887 if( $wit->is_layered ) {
888 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
889 $wit->sigil.$self->ac_label );
890 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
891 push( @{$table->{'alignment'}},
892 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
898 sub _make_witness_row {
899 my( $path, $positions, $noderefs ) = @_;
901 map { $char_hash{$_} = undef } @$positions;
903 foreach my $rdg ( @$path ) {
904 my $rtext = $rdg->text;
905 $rtext = '#LACUNA#' if $rdg->is_lacuna;
906 print STDERR "rank " . $rdg->rank . "\n" if $debug;
907 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
908 $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
911 my @row = map { $char_hash{$_} } @$positions;
912 # Fill in lacuna markers for undef spots in the row
913 my $last_el = shift @row;
914 my @filled_row = ( $last_el );
915 foreach my $el ( @row ) {
916 # If we are using node reference, make the lacuna node appear many times
917 # in the table. If not, use the lacuna tag.
918 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
919 $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
921 push( @filled_row, $el );
927 # Tiny utility function to say if a table element is a lacuna
930 return 1 if $el->{'t'} eq '#LACUNA#';
931 return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
932 && $el->{'t'}->is_lacuna;
936 # Helper to turn the witnesses along columns rather than rows. Assumes
941 return $result unless scalar @$table;
942 my $nrows = scalar @{$table->[0]};
943 foreach my $idx ( 0 .. $nrows - 1 ) {
944 foreach my $wit ( 0 .. $#{$table} ) {
945 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
951 =head1 NAVIGATION METHODS
953 =head2 reading_sequence( $first, $last, $sigil, $backup )
955 Returns the ordered list of readings, starting with $first and ending
956 with $last, for the witness given in $sigil. If a $backup sigil is
957 specified (e.g. when walking a layered witness), it will be used wherever
958 no $sigil path exists. If there is a base text reading, that will be
959 used wherever no path exists for $sigil or $backup.
963 # TODO Think about returning some lazy-eval iterator.
964 # TODO Get rid of backup; we should know from what witness is whether we need it.
966 sub reading_sequence {
967 my( $self, $start, $end, $witness ) = @_;
969 $witness = $self->baselabel unless $witness;
970 my @readings = ( $start );
973 while( $n && $n->id ne $end->id ) {
974 if( exists( $seen{$n->id} ) ) {
975 throw( "Detected loop for $witness at " . $n->id );
979 my $next = $self->next_reading( $n, $witness );
981 throw( "Did not find any path for $witness from reading " . $n->id );
983 push( @readings, $next );
986 # Check that the last reading is our end reading.
987 my $last = $readings[$#readings];
988 throw( "Last reading found from " . $start->text .
989 " for witness $witness is not the end!" ) # TODO do we get this far?
990 unless $last->id eq $end->id;
995 =head2 next_reading( $reading, $sigil );
997 Returns the reading that follows the given reading along the given witness
1003 # Return the successor via the corresponding path.
1005 my $answer = $self->_find_linked_reading( 'next', @_ );
1006 return undef unless $answer;
1007 return $self->reading( $answer );
1010 =head2 prior_reading( $reading, $sigil )
1012 Returns the reading that precedes the given reading along the given witness
1018 # Return the predecessor via the corresponding path.
1020 my $answer = $self->_find_linked_reading( 'prior', @_ );
1021 return $self->reading( $answer );
1024 sub _find_linked_reading {
1025 my( $self, $direction, $node, $path ) = @_;
1027 # Get a backup if we are dealing with a layered witness
1029 my $aclabel = $self->ac_label;
1030 if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
1034 my @linked_paths = $direction eq 'next'
1035 ? $self->sequence->edges_from( $node )
1036 : $self->sequence->edges_to( $node );
1037 return undef unless scalar( @linked_paths );
1039 # We have to find the linked path that contains all of the
1040 # witnesses supplied in $path.
1041 my( @path_wits, @alt_path_wits );
1042 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1043 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1046 foreach my $le ( @linked_paths ) {
1047 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1050 my @le_wits = sort $self->path_witnesses( $le );
1051 if( _is_within( \@path_wits, \@le_wits ) ) {
1052 # This is the right path.
1053 return $direction eq 'next' ? $le->[1] : $le->[0];
1054 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1058 # Got this far? Return the alternate path if it exists.
1059 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1062 # Got this far? Return the base path if it exists.
1063 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1066 # Got this far? We have no appropriate path.
1067 warn "Could not find $direction node from " . $node->id
1068 . " along path $path";
1074 my( $set1, $set2 ) = @_;
1075 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1076 foreach my $el ( @$set1 ) {
1077 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1082 # Return the string that joins together a list of witnesses for
1083 # display on a single path.
1084 sub _witnesses_of_label {
1085 my( $self, $label ) = @_;
1086 my $regex = $self->wit_list_separator;
1087 my @answer = split( /\Q$regex\E/, $label );
1091 =head2 path_text( $sigil, $mainsigil [, $start, $end ] )
1093 Returns the text of a witness (plus its backup, if we are using a layer)
1094 as stored in the collation. The text is returned as a string, where the
1095 individual readings are joined with spaces and the meta-readings (e.g.
1096 lacunae) are omitted. Optional specification of $start and $end allows
1097 the generation of a subset of the witness text.
1102 my( $self, $wit, $start, $end ) = @_;
1103 $start = $self->start unless $start;
1104 $end = $self->end unless $end;
1105 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
1106 return join( ' ', map { $_->text } @path );
1109 =head1 INITIALIZATION METHODS
1111 These are mostly for use by parsers.
1113 =head2 make_witness_path( $witness )
1115 Link the array of readings contained in $witness->path (and in
1116 $witness->uncorrected_path if it exists) into collation paths.
1117 Clear out the arrays when finished.
1119 =head2 make_witness_paths
1121 Call make_witness_path for all witnesses in the tradition.
1125 # For use when a collation is constructed from a base text and an apparatus.
1126 # We have the sequences of readings and just need to add path edges.
1127 # When we are done, clear out the witness path attributes, as they are no
1129 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1131 sub make_witness_paths {
1133 foreach my $wit ( $self->tradition->witnesses ) {
1134 # print STDERR "Making path for " . $wit->sigil . "\n";
1135 $self->make_witness_path( $wit );
1139 sub make_witness_path {
1140 my( $self, $wit ) = @_;
1141 my @chain = @{$wit->path};
1142 my $sig = $wit->sigil;
1143 foreach my $idx ( 0 .. $#chain-1 ) {
1144 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1146 if( $wit->is_layered ) {
1147 @chain = @{$wit->uncorrected_path};
1148 foreach my $idx( 0 .. $#chain-1 ) {
1149 my $source = $chain[$idx];
1150 my $target = $chain[$idx+1];
1151 $self->add_path( $source, $target, $sig.$self->ac_label )
1152 unless $self->has_path( $source, $target, $sig );
1156 $wit->clear_uncorrected_path;
1159 =head2 calculate_ranks
1161 Calculate the reading ranks (that is, their aligned positions relative
1162 to each other) for the graph. This can only be called on linear collations.
1166 sub calculate_ranks {
1168 # Walk a version of the graph where every node linked by a relationship
1169 # edge is fundamentally the same node, and do a topological ranking on
1170 # the nodes in this graph.
1171 my $topo_graph = Graph->new();
1175 foreach my $r ( $self->readings ) {
1176 next if exists $rel_containers{$r->id};
1177 my @rels = $r->related_readings( 'colocated' );
1179 # Make a relationship container.
1181 my $rn = 'rel_container_' . $rel_ctr++;
1182 $topo_graph->add_vertex( $rn );
1184 $rel_containers{$_->id} = $rn;
1187 # Add a new node to mirror the old node.
1188 $rel_containers{$r->id} = $r->id;
1189 $topo_graph->add_vertex( $r->id );
1194 foreach my $r ( $self->readings ) {
1195 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1196 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1197 $rel_containers{$n} );
1198 # $DB::single = 1 unless $tfrom && $tto;
1199 $topo_graph->add_edge( $tfrom, $tto );
1203 # Now do the rankings, starting with the start node.
1204 my $topo_start = $rel_containers{$self->start->id};
1205 my $node_ranks = { $topo_start => 0 };
1206 my @curr_origin = ( $topo_start );
1207 # A little iterative function.
1208 while( @curr_origin ) {
1209 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1211 # Transfer our rankings from the topological graph to the real one.
1212 foreach my $r ( $self->readings ) {
1213 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1214 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1216 # Die. Find the last rank we calculated.
1217 my @all_defined = sort { $node_ranks->{$rel_containers{$a->id}}
1218 <=> $node_ranks->{$rel_containers{$b->id}} }
1220 my $last = pop @all_defined;
1221 throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
1227 my( $graph, $node_ranks, @current_nodes ) = @_;
1228 # Look at each of the children of @current_nodes. If all the child's
1229 # parents have a rank, assign it the highest rank + 1 and add it to
1230 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1231 # parent gets a rank.
1233 foreach my $c ( @current_nodes ) {
1234 warn "Current reading $c has no rank!"
1235 unless exists $node_ranks->{$c};
1236 # print STDERR "Looking at child of node $c, rank "
1237 # . $node_ranks->{$c} . "\n";
1238 foreach my $child ( $graph->successors( $c ) ) {
1239 next if exists $node_ranks->{$child};
1240 my $highest_rank = -1;
1242 foreach my $parent ( $graph->predecessors( $child ) ) {
1243 if( exists $node_ranks->{$parent} ) {
1244 $highest_rank = $node_ranks->{$parent}
1245 if $highest_rank <= $node_ranks->{$parent};
1252 my $c_rank = $highest_rank + 1;
1253 # print STDERR "Assigning rank $c_rank to node $child \n";
1254 $node_ranks->{$child} = $c_rank;
1255 push( @next_nodes, $child );
1261 =head2 flatten_ranks
1263 A convenience method for parsing collation data. Searches the graph for readings
1264 with the same text at the same rank, and merges any that are found.
1270 my %unique_rank_rdg;
1271 foreach my $rdg ( $self->readings ) {
1272 next unless $rdg->has_rank;
1273 my $key = $rdg->rank . "||" . $rdg->text;
1274 if( exists $unique_rank_rdg{$key} ) {
1276 # print STDERR "Combining readings at same rank: $key\n";
1277 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1279 $unique_rank_rdg{$key} = $rdg;
1284 =head2 text_from_paths
1286 Calculate the text array for all witnesses from the path, for later consistency
1287 checking. Only to be used if there is no non-graph-based way to know the
1292 sub text_from_paths {
1294 foreach my $wit ( $self->tradition->witnesses ) {
1295 my @text = split( /\s+/,
1296 $self->reading_sequence( $self->start, $self->end, $wit->sigil ) );
1297 $wit->text( \@text );
1298 if( $wit->is_layered ) {
1299 my @uctext = split( /\s+/,
1300 $self->reading_sequence( $self->start, $self->end,
1301 $wit->sigil.$self->ac_label ) );
1302 $wit->text( \@uctext );
1307 =head1 UTILITY FUNCTIONS
1309 =head2 common_predecessor( $reading_a, $reading_b )
1311 Find the last reading that occurs in sequence before both the given readings.
1313 =head2 common_successor( $reading_a, $reading_b )
1315 Find the first reading that occurs in sequence after both the given readings.
1319 use Text::Tradition;
1321 my $cxfile = 't/data/Collatex-16.xml';
1322 my $t = Text::Tradition->new(
1324 'input' => 'CollateX',
1327 my $c = $t->collation;
1329 is( $c->common_predecessor( 'n9', 'n23' )->id,
1330 'n20', "Found correct common predecessor" );
1331 is( $c->common_successor( 'n9', 'n23' )->id,
1332 '#END#', "Found correct common successor" );
1334 is( $c->common_predecessor( 'n19', 'n17' )->id,
1335 'n16', "Found correct common predecessor for readings on same path" );
1336 is( $c->common_successor( 'n21', 'n26' )->id,
1337 '#END#', "Found correct common successor for readings on same path" );
1343 ## Return the closest reading that is a predecessor of both the given readings.
1344 sub common_predecessor {
1346 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1347 return $self->common_in_path( $r1, $r2, 'predecessors' );
1350 sub common_successor {
1352 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1353 return $self->common_in_path( $r1, $r2, 'successors' );
1356 sub common_in_path {
1357 my( $self, $r1, $r2, $dir ) = @_;
1358 my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
1359 $iter = $self->end->rank - $iter if $dir eq 'successors';
1361 my @last_checked = ( $r1, $r2 );
1363 while( !@candidates ) {
1365 foreach my $lc ( @last_checked ) {
1366 foreach my $p ( $lc->$dir ) {
1367 if( $all_seen{$p->id} ) {
1368 push( @candidates, $p );
1370 $all_seen{$p->id} = 1;
1371 push( @new_lc, $p );
1375 @last_checked = @new_lc;
1377 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1378 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1382 Text::Tradition::Error->throw(
1383 'ident' => 'Collation error',
1389 __PACKAGE__->meta->make_immutable;
1395 =item * Get rid of $backup in reading_sequence