1 package Text::Tradition::Collation;
3 use Encode qw( decode_utf8 );
6 use IPC::Run qw( run binary );
8 use Text::Tradition::Collation::Reading;
15 default => sub { Graph->new() },
24 default => sub { Graph->new( undirected => 1 ) },
26 relationships => 'edges',
32 isa => 'Text::Tradition',
37 isa => 'HashRef[Text::Tradition::Collation::Reading]',
41 _add_reading => 'set',
42 del_reading => 'delete',
43 has_reading => 'exists',
46 default => sub { {} },
49 has 'wit_list_separator' => (
58 default => 'base text',
75 isa => 'Text::Tradition::Collation::Reading',
76 writer => '_set_start',
82 isa => 'Text::Tradition::Collation::Reading',
87 # The collation can be created two ways:
88 # 1. Collate a set of witnesses (with CollateX I guess) and process
89 # the results as in 2.
90 # 2. Read a pre-prepared collation in one of a variety of formats,
91 # and make the graph from that.
93 # The graph itself will (for now) be immutable, and the positions
94 # within the graph will also be immutable. We need to calculate those
95 # positions upon graph construction. The equivalences between graph
96 # nodes will be mutable, entirely determined by the user (or possibly
97 # by some semantic pre-processing provided by the user.) So the
98 # constructor should just make an empty equivalences object. The
99 # constructor will also need to make the witness objects, if we didn't
100 # come through option 1.
104 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
105 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
108 ### Reading construct/destruct functions
111 my( $self, $reading ) = @_;
112 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
113 my %args = %$reading;
114 $reading = Text::Tradition::Collation::Reading->new(
115 'collation' => $self,
118 # First check to see if a reading with this ID exists.
119 if( $self->reading( $reading->id ) ) {
120 warn "Collation already has a reading with id " . $reading->id;
123 $self->_add_reading( $reading->id => $reading );
124 # Once the reading has been added, put it in both graphs.
125 $self->sequence->add_vertex( $reading->id );
126 $self->relations->add_vertex( $reading->id );
130 around del_reading => sub {
135 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
138 # Remove the reading from the graphs.
139 $self->sequence->delete_vertex( $arg );
140 $self->relations->delete_vertex( $arg );
143 $self->$orig( $arg );
146 # merge_readings( $main, $to_be_deleted );
151 # We only need the IDs for adding paths to the graph, not the reading
152 # objects themselves.
153 my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
155 # The kept reading should inherit the paths and the relationships
156 # of the deleted reading.
157 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
158 my @vector = ( $kept );
159 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
160 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
161 next if $vector[0] eq $vector[1]; # Don't add a self loop
162 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
163 $self->sequence->add_edge( @vector );
164 my $fwits = $self->sequence->get_edge_attributes( @vector );
165 @wits{keys %$fwits} = values %$fwits;
166 $self->sequence->set_edge_attributes( @vector, \%wits );
168 foreach my $rel ( $self->relations->edges_at( $deleted ) ) {
169 my @vector = ( $kept );
170 push( @vector, $rel->[0] eq $deleted ? $rel->[1] : $rel->[0] );
171 next if $vector[0] eq $vector[1]; # Don't add a self loop
172 # Is there a relationship here already? If so, keep it.
173 # TODO Warn about conflicting relationships
174 next if $self->relations->has_edge( @vector );
175 # If not, adopt the relationship that would be deleted.
176 $self->relations->add_edge( @vector );
177 my $attr = $self->relations->get_edge_attributes( @$rel );
178 $self->relations->set_edge_attributes( @vector, $attr );
181 # Do the deletion deed.
182 if( $combine_char ) {
183 my $kept_obj = $self->reading( $kept );
184 my $new_text = join( $combine_char, $kept_obj->text,
185 $self->reading( $deleted )->text );
186 $kept_obj->alter_text( $new_text );
188 $self->del_reading( $deleted );
192 # Helper function for manipulating the graph.
193 sub _stringify_args {
194 my( $self, $first, $second, $arg ) = @_;
196 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
197 $second = $second->id
198 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
199 return( $first, $second, $arg );
207 # We only need the IDs for adding paths to the graph, not the reading
208 # objects themselves.
209 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
211 # Connect the readings
212 $self->sequence->add_edge( $source, $target );
213 # Note the witness in question
214 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
220 if( ref( $_[0] ) eq 'ARRAY' ) {
227 # We only need the IDs for adding paths to the graph, not the reading
228 # objects themselves.
229 my( $source, $target, $wit ) = $self->_stringify_args( @args );
231 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
232 $self->sequence->delete_edge_attribute( $source, $target, $wit );
234 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
235 $self->sequence->delete_edge( $source, $target );
240 # Extra graph-alike utility
243 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
244 return undef unless $self->sequence->has_edge( $source, $target );
245 return $self->sequence->has_edge_attribute( $source, $target, $wit );
248 ### Relationship logic
250 =head2 add_relationship( $reading1, $reading2, $definition )
252 Adds the specified relationship between the two readings. A relationship
253 is transitive (i.e. undirected), and must have the following attributes
254 specified in the hashref $definition:
258 =item * type - Can be one of spelling, orthographic, grammatical, meaning, lexical, collated, repetition, transposition. All but the last two are only valid relationships between readings that occur at the same point in the text.
260 =item * non_correctable - (Optional) True if the reading would not have been corrected independently.
262 =item * non_independent - (Optional) True if the variant is unlikely to have occurred independently in unrelated witnesses.
264 =item * global - (Optional) A meta-attribute, to set the same relationship between readings with the same text whenever they occur in the same place.
270 # Wouldn't it be lovely if edges could be objects, and all this type checking
271 # and attribute management could be done via Moose?
273 sub add_relationship {
275 my( $source, $target, $options ) = $self->_stringify_args( @_ );
278 if( !defined $options->{'type'} ||
279 $options->{'type'} !~ /^(spelling|orthographic|grammatical|meaning|lexical|collated|repetition|transposition)$/i ) {
280 my $t = $options->{'type'} ? $options->{'type'} : '';
281 return( undef, "Invalid or missing type " . $options->{'type'} );
283 unless ( $options->{'type'} =~ /^(repetition|transposition)$/ ) {
284 $options->{'colocated'} = 1;
287 # Make sure there is not another relationship between these two
289 if( $self->relations->has_edge( $source, $target ) ) {
290 return ( undef, "Relationship already exists between these readings" );
292 if( !$self->relationship_valid( $source, $target, $options->{'type'} ) ) {
293 return ( undef, 'Relationship creates witness loop' );
296 my @vector = ( $source, $target );
297 $self->relations->add_edge( @vector );
298 $self->relations->set_edge_attributes( @vector, $options );
300 # TODO Handle global relationship setting
302 return( 1, @vector );
305 sub relationship_valid {
306 my( $self, $source, $target, $rel ) = @_;
307 if( $rel eq 'repetition' ) {
309 } elsif ( $rel eq 'transposition' ) {
310 # Check that the two readings do not appear in the same witness.
312 map { $seen_wits{$_} = 1 } $self->reading_witnesses( $source );
313 foreach my $w ( $self->reading_witnesses( $target ) ) {
314 return 0 if $seen_wits{$w};
318 # Check that linking the source and target in a relationship won't lead
319 # to a path loop for any witness. First make a lookup table of all the
320 # readings related to either the source or the target.
321 my @proposed_related = ( $source, $target );
322 push( @proposed_related, $self->related_readings( $source, 'colocated' ) );
323 push( @proposed_related, $self->related_readings( $target, 'colocated' ) );
325 map { $pr_ids{ $_ } = 1 } @proposed_related;
327 # None of these proposed related readings should have a neighbor that
328 # is also in proposed_related.
329 foreach my $pr ( keys %pr_ids ) {
330 foreach my $neighbor( $self->sequence->neighbors( $pr ) ) {
331 return 0 if exists $pr_ids{$neighbor};
338 # Return a list of the witnesses in which the reading appears.
339 sub reading_witnesses {
340 my( $self, $reading ) = @_;
341 # We need only check either the incoming or the outgoing edges; I have
342 # arbitrarily chosen "incoming". Thus, special-case the start node.
343 if( $reading eq $self->start ) {
344 return map { $_->sigil } $self->tradition->witnesses;
347 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
348 my $wits = $self->sequence->get_edge_attributes( @$e );
349 @all_witnesses{ keys %$wits } = 1;
351 return keys %all_witnesses;
354 sub related_readings {
355 my( $self, $reading, $colocated ) = @_;
357 if( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
358 $reading = $reading->id;
360 # print STDERR "Returning related objects\n";
362 # print STDERR "Returning related object names\n";
364 my @related = $self->relations->all_reachable( $reading );
366 my @colo = grep { $self->relations->has_edge_attribute( $reading, $_, 'colocated' ) } @related;
369 return $return_object ? map { $self->reading( $_ ) } @related : @related;
372 =head2 Output method(s)
378 print $graph->as_svg( $recalculate );
380 Returns an SVG string that represents the graph, via as_dot and graphviz.
387 my @cmd = qw/dot -Tsvg/;
389 my $dotfile = File::Temp->new();
391 # $dotfile->unlink_on_destroy(0);
392 binmode $dotfile, ':utf8';
393 print $dotfile $self->as_dot();
394 push( @cmd, $dotfile->filename );
395 run( \@cmd, ">", binary(), \$svg );
396 $svg = decode_utf8( $svg );
402 print $graph->as_dot( $view, $recalculate );
404 Returns a string that is the collation graph expressed in dot
405 (i.e. GraphViz) format. The 'view' argument determines what kind of
407 * 'path': a graph of witness paths through the collation (DEFAULT)
408 * 'relationship': a graph of how collation readings relate to
414 my( $self, $view ) = @_;
415 $view = 'sequence' unless $view;
416 # TODO consider making some of these things configurable
417 my $graph_name = $self->tradition->name;
418 $graph_name =~ s/[^\w\s]//g;
419 $graph_name = join( '_', split( /\s+/, $graph_name ) );
420 my $dot = sprintf( "digraph %s {\n", $graph_name );
421 $dot .= "\tedge [ arrowhead=open ];\n";
422 $dot .= "\tgraph [ rankdir=LR ];\n";
423 $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
424 11, "white", "filled", "ellipse" );
426 foreach my $reading ( $self->readings ) {
427 # Need not output nodes without separate labels
428 next if $reading->id eq $reading->text;
429 my $label = $reading->text;
430 $label =~ s/\"/\\\"/g;
431 $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
434 # TODO do something sensible for relationships
436 my @edges = $self->paths;
437 foreach my $edge ( @edges ) {
438 my %variables = ( 'color' => '#000000',
439 'fontcolor' => '#000000',
440 'label' => join( ', ', $self->path_display_label( $edge ) ),
442 my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
443 # Account for the rank gap if necessary
444 my $rankgap = $self->reading( $edge->[1] )->rank
445 - $self->reading( $edge->[0] )->rank;
446 $varopts .= ", minlen=$rankgap" if $rankgap > 1;
447 $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
448 $edge->[0], $edge->[1], $varopts );
455 my( $self, @edge ) = @_;
456 # If edge is an arrayref, cope.
457 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
461 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
465 sub path_display_label {
466 my( $self, $edge ) = @_;
467 my @wits = $self->path_witnesses( $edge );
468 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
469 if( scalar @wits > $maj ) {
472 return join( ', ', @wits );
479 print $graph->as_graphml( $recalculate )
481 Returns a GraphML representation of the collation graph, with
482 transposition information and position information. Unless
483 $recalculate is passed (and is a true value), the method will return a
484 cached copy of the SVG after the first call to the method.
492 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
493 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
494 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
495 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
497 # Create the document and root node
498 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
499 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
500 $graphml->setDocumentElement( $root );
501 $root->setNamespace( $xsi_ns, 'xsi', 0 );
502 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
504 # Add the data keys for the graph
507 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
508 foreach my $datum ( @graph_attributes ) {
509 $graph_data_keys{$datum} = 'dg'.$gdi++;
510 my $key = $root->addNewChild( $graphml_ns, 'key' );
511 $key->setAttribute( 'attr.name', $datum );
512 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
513 $key->setAttribute( 'for', 'graph' );
514 $key->setAttribute( 'id', $graph_data_keys{$datum} );
517 # Add the data keys for nodes
524 is_start => 'boolean',
526 is_lacuna => 'boolean',
528 foreach my $datum ( keys %node_data ) {
529 $node_data_keys{$datum} = 'dn'.$ndi++;
530 my $key = $root->addNewChild( $graphml_ns, 'key' );
531 $key->setAttribute( 'attr.name', $datum );
532 $key->setAttribute( 'attr.type', $node_data{$datum} );
533 $key->setAttribute( 'for', 'node' );
534 $key->setAttribute( 'id', $node_data_keys{$datum} );
537 # Add the data keys for edges, i.e. witnesses
541 witness => 'string', # ID/label for a path
542 relationship => 'string', # ID/label for a relationship
543 extra => 'boolean', # Path key
544 colocated => 'boolean', # Relationship key
545 non_correctable => 'boolean', # Relationship key
546 non_independent => 'boolean', # Relationship key
548 foreach my $datum ( keys %edge_data ) {
549 $edge_data_keys{$datum} = 'de'.$edi++;
550 my $key = $root->addNewChild( $graphml_ns, 'key' );
551 $key->setAttribute( 'attr.name', $datum );
552 $key->setAttribute( 'attr.type', $edge_data{$datum} );
553 $key->setAttribute( 'for', 'edge' );
554 $key->setAttribute( 'id', $edge_data_keys{$datum} );
557 # Add the collation graphs themselves
558 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
559 $sgraph->setAttribute( 'edgedefault', 'directed' );
560 $sgraph->setAttribute( 'id', $self->tradition->name );
561 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
562 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
563 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
564 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
565 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
567 my $rgraph = $root->addNewChild( $graphml_ns, 'graph' );
568 $rgraph->setAttribute( 'edgedefault', 'undirected' );
569 $rgraph->setAttribute( 'id', 'relationships' );
570 $rgraph->setAttribute( 'parse.edgeids', 'canonical' );
571 $rgraph->setAttribute( 'parse.edges', scalar($self->relationships) );
572 $rgraph->setAttribute( 'parse.nodeids', 'canonical' );
573 $rgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
574 $rgraph->setAttribute( 'parse.order', 'nodesfirst' );
576 # Collation attribute data
577 foreach my $datum ( @graph_attributes ) {
578 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
579 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
584 # Add our readings to the graphs
585 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
586 # Add to the main graph
587 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
588 my $node_xmlid = 'n' . $node_ctr++;
589 $node_hash{ $n->id } = $node_xmlid;
590 $node_el->setAttribute( 'id', $node_xmlid );
591 foreach my $d ( keys %node_data ) {
593 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
596 # Add to the relationships graph
597 my $rnode_el = $rgraph->addNewChild( $graphml_ns, 'node' );
598 $rnode_el->setAttribute( 'id', $node_xmlid );
601 # Add the path edges to the sequence graph
603 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
604 # We add an edge in the graphml for every witness in $e.
605 foreach my $wit ( $self->path_witnesses( $e ) ) {
606 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
607 $node_hash{ $e->[0] },
608 $node_hash{ $e->[1] } );
609 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
610 $edge_el->setAttribute( 'source', $from );
611 $edge_el->setAttribute( 'target', $to );
612 $edge_el->setAttribute( 'id', $id );
614 # It's a witness path, so add the witness
616 my $key = $edge_data_keys{'witness'};
617 # Is this an ante-corr witness?
618 my $aclabel = $self->ac_label;
619 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
620 # Keep the base witness
622 # ...and record that this is an 'extra' reading path
623 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
625 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
629 # Add the relationship edges to the relationships graph
630 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->relationships ) {
631 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
632 $node_hash{ $e->[0] },
633 $node_hash{ $e->[1] } );
634 my $edge_el = $rgraph->addNewChild( $graphml_ns, 'edge' );
635 $edge_el->setAttribute( 'source', $from );
636 $edge_el->setAttribute( 'target', $to );
637 $edge_el->setAttribute( 'id', $id );
639 my $data = $self->relations->get_edge_attributes( @$e );
640 # It's a relationship, so save the relationship data
641 _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $data->{type} );
642 _add_graphml_data( $edge_el, $edge_data_keys{'colocated'}, $data->{colocated} );
643 if( exists $data->{non_correctable} ) {
644 _add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'},
645 $data->{non_correctable} );
647 if( exists $data->{non_independent} ) {
648 _add_graphml_data( $edge_el, $edge_data_keys{'non_independent'},
649 $data->{non_independent} );
653 # Save and return the thing
654 my $result = decode_utf8( $graphml->toString(1) );
658 sub _add_graphml_data {
659 my( $el, $key, $value ) = @_;
660 return unless defined $value;
661 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
662 $data_el->setAttribute( 'key', $key );
663 $data_el->appendText( $value );
668 print $graph->as_csv( $recalculate )
670 Returns a CSV alignment table representation of the collation graph, one
671 row per witness (or witness uncorrected.)
677 my $table = $self->make_alignment_table;
678 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
680 # Make the header row
681 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
682 push( @result, decode_utf8( $csv->string ) );
683 # Make the rest of the rows
684 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
685 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
686 my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
687 $csv->combine( @row );
688 push( @result, decode_utf8( $csv->string ) );
690 return join( "\n", @result );
693 =item B<make_alignment_table>
695 my $table = $graph->make_alignment_table( $use_refs, \@wits_to_include )
697 Return a reference to an alignment table, in a slightly enhanced CollateX
698 format which looks like this:
700 $table = { alignment => [ { witness => "SIGIL",
701 tokens => [ { t => "READINGTEXT" }, ... ] },
703 tokens => [ { t => "READINGTEXT" }, ... ] },
707 If $use_refs is set to 1, the reading object is returned in the table
708 instead of READINGTEXT; if not, the text of the reading is returned.
709 If $wits_to_include is set to a hashref, only the witnesses whose sigil
710 keys have a true hash value will be included.
714 sub make_alignment_table {
715 my( $self, $noderefs, $include ) = @_;
716 unless( $self->linear ) {
717 warn "Need a linear graph in order to make an alignment table";
720 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
721 my @all_pos = ( 1 .. $self->end->rank - 1 );
722 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
724 next unless $include->{$wit->sigil};
726 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
727 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
728 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
729 push( @{$table->{'alignment'}},
730 { 'witness' => $wit->sigil, 'tokens' => \@row } );
731 if( $wit->is_layered ) {
732 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
733 $wit->sigil.$self->ac_label, $wit->sigil );
734 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
735 push( @{$table->{'alignment'}},
736 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
742 sub _make_witness_row {
743 my( $path, $positions, $noderefs ) = @_;
745 map { $char_hash{$_} = undef } @$positions;
747 foreach my $rdg ( @$path ) {
748 my $rtext = $rdg->text;
749 $rtext = '#LACUNA#' if $rdg->is_lacuna;
750 print STDERR "rank " . $rdg->rank . "\n" if $debug;
751 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
752 $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
755 my @row = map { $char_hash{$_} } @$positions;
756 # Fill in lacuna markers for undef spots in the row
757 my $last_el = shift @row;
758 my @filled_row = ( $last_el );
759 foreach my $el ( @row ) {
760 # If we are using node reference, make the lacuna node appear many times
761 # in the table. If not, use the lacuna tag.
762 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
763 $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
765 push( @filled_row, $el );
771 # Tiny utility function to say if a table element is a lacuna
774 return 1 if $el->{'t'} eq '#LACUNA#';
775 return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
776 && $el->{'t'}->is_lacuna;
780 # Helper to turn the witnesses along columns rather than rows. Assumes
785 return $result unless scalar @$table;
786 my $nrows = scalar @{$table->[0]};
787 foreach my $idx ( 0 .. $nrows - 1 ) {
788 foreach my $wit ( 0 .. $#{$table} ) {
789 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
797 =head2 Navigation methods
803 my $beginning = $collation->start();
805 Returns the beginning of the collation, a meta-reading with label '#START#'.
809 my $end = $collation->end();
811 Returns the end of the collation, a meta-reading with label '#END#'.
814 =item B<reading_sequence>
816 my @readings = $graph->reading_sequence( $first, $last, $path[, $alt_path] );
818 Returns the ordered list of readings, starting with $first and ending
819 with $last, along the given witness path. If no path is specified,
820 assume that the path is that of the base text (if any.)
824 # TODO Think about returning some lazy-eval iterator.
826 sub reading_sequence {
827 my( $self, $start, $end, $witness, $backup ) = @_;
829 $witness = $self->baselabel unless $witness;
830 my @readings = ( $start );
833 while( $n && $n->id ne $end->id ) {
834 if( exists( $seen{$n->id} ) ) {
835 warn "Detected loop at " . $n->id;
840 my $next = $self->next_reading( $n, $witness, $backup );
842 warn "Did not find any path for $witness from reading " . $n->id;
845 push( @readings, $next );
848 # Check that the last reading is our end reading.
849 my $last = $readings[$#readings];
850 warn "Last reading found from " . $start->text .
851 " for witness $witness is not the end!"
852 unless $last->id eq $end->id;
857 =item B<next_reading>
859 my $next_reading = $graph->next_reading( $reading, $witpath );
861 Returns the reading that follows the given reading along the given witness
867 # Return the successor via the corresponding path.
869 my $answer = $self->_find_linked_reading( 'next', @_ );
870 return undef unless $answer;
871 return $self->reading( $answer );
874 =item B<prior_reading>
876 my $prior_reading = $graph->prior_reading( $reading, $witpath );
878 Returns the reading that precedes the given reading along the given witness
884 # Return the predecessor via the corresponding path.
886 my $answer = $self->_find_linked_reading( 'prior', @_ );
887 return $self->reading( $answer );
890 sub _find_linked_reading {
891 my( $self, $direction, $node, $path, $alt_path ) = @_;
892 my @linked_paths = $direction eq 'next'
893 ? $self->sequence->edges_from( $node )
894 : $self->sequence->edges_to( $node );
895 return undef unless scalar( @linked_paths );
897 # We have to find the linked path that contains all of the
898 # witnesses supplied in $path.
899 my( @path_wits, @alt_path_wits );
900 @path_wits = sort( $self->witnesses_of_label( $path ) ) if $path;
901 @alt_path_wits = sort( $self->witnesses_of_label( $alt_path ) ) if $alt_path;
904 foreach my $le ( @linked_paths ) {
905 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
908 my @le_wits = $self->path_witnesses( $le );
909 if( _is_within( \@path_wits, \@le_wits ) ) {
910 # This is the right path.
911 return $direction eq 'next' ? $le->[1] : $le->[0];
912 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
916 # Got this far? Return the alternate path if it exists.
917 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
920 # Got this far? Return the base path if it exists.
921 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
924 # Got this far? We have no appropriate path.
925 warn "Could not find $direction node from " . $node->id
926 . " along path $path";
932 my( $set1, $set2 ) = @_;
933 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
934 foreach my $el ( @$set1 ) {
935 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
941 ## INITIALIZATION METHODS - for use by parsers
943 # For use when a collation is constructed from a base text and an apparatus.
944 # We have the sequences of readings and just need to add path edges.
945 # When we are done, clear out the witness path attributes, as they are no
947 # TODO Find a way to replace the witness path attributes with encapsulated functions?
949 sub make_witness_paths {
951 foreach my $wit ( $self->tradition->witnesses ) {
952 # print STDERR "Making path for " . $wit->sigil . "\n";
953 $self->make_witness_path( $wit );
957 sub make_witness_path {
958 my( $self, $wit ) = @_;
959 my @chain = @{$wit->path};
960 my $sig = $wit->sigil;
961 foreach my $idx ( 0 .. $#chain-1 ) {
962 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
964 if( $wit->is_layered ) {
965 @chain = @{$wit->uncorrected_path};
966 foreach my $idx( 0 .. $#chain-1 ) {
967 my $source = $chain[$idx];
968 my $target = $chain[$idx+1];
969 $self->add_path( $source, $target, $sig.$self->ac_label )
970 unless $self->has_path( $source, $target, $sig );
974 $wit->clear_uncorrected_path;
977 sub calculate_ranks {
979 # Walk a version of the graph where every node linked by a relationship
980 # edge is fundamentally the same node, and do a topological ranking on
981 # the nodes in this graph.
982 my $topo_graph = Graph->new();
986 foreach my $r ( $self->readings ) {
987 next if exists $rel_containers{$r->id};
988 my @rels = $r->related_readings( 'colocated' );
990 # Make a relationship container.
992 my $rn = 'rel_container_' . $rel_ctr++;
993 $topo_graph->add_vertex( $rn );
995 $rel_containers{$_->id} = $rn;
998 # Add a new node to mirror the old node.
999 $rel_containers{$r->id} = $r->id;
1000 $topo_graph->add_vertex( $r->id );
1005 foreach my $r ( $self->readings ) {
1006 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1007 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1008 $rel_containers{$n} );
1009 $DB::single = 1 unless $tfrom && $tto;
1010 $topo_graph->add_edge( $tfrom, $tto );
1014 # Now do the rankings, starting with the start node.
1015 my $topo_start = $rel_containers{$self->start->id};
1016 my $node_ranks = { $topo_start => 0 };
1017 my @curr_origin = ( $topo_start );
1018 # A little iterative function.
1019 while( @curr_origin ) {
1020 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1022 # Transfer our rankings from the topological graph to the real one.
1023 foreach my $r ( $self->readings ) {
1024 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1025 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1028 die "No rank calculated for node " . $r->id
1029 . " - do you have a cycle in the graph?";
1035 my( $graph, $node_ranks, @current_nodes ) = @_;
1036 # Look at each of the children of @current_nodes. If all the child's
1037 # parents have a rank, assign it the highest rank + 1 and add it to
1038 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1039 # parent gets a rank.
1041 foreach my $c ( @current_nodes ) {
1042 warn "Current reading $c has no rank!"
1043 unless exists $node_ranks->{$c};
1044 # print STDERR "Looking at child of node $c, rank "
1045 # . $node_ranks->{$c} . "\n";
1046 foreach my $child ( $graph->successors( $c ) ) {
1047 next if exists $node_ranks->{$child};
1048 my $highest_rank = -1;
1050 foreach my $parent ( $graph->predecessors( $child ) ) {
1051 if( exists $node_ranks->{$parent} ) {
1052 $highest_rank = $node_ranks->{$parent}
1053 if $highest_rank <= $node_ranks->{$parent};
1060 my $c_rank = $highest_rank + 1;
1061 # print STDERR "Assigning rank $c_rank to node $child \n";
1062 $node_ranks->{$child} = $c_rank;
1063 push( @next_nodes, $child );
1069 # Another method to make up for rough collation methods. If the same reading
1070 # appears multiple times at the same rank, collapse the nodes.
1073 my %unique_rank_rdg;
1074 foreach my $rdg ( $self->readings ) {
1075 next unless $rdg->has_rank;
1076 my $key = $rdg->rank . "||" . $rdg->text;
1077 if( exists $unique_rank_rdg{$key} ) {
1079 # print STDERR "Combining readings at same rank: $key\n";
1080 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1082 $unique_rank_rdg{$key} = $rdg;
1088 ## Utility functions
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 );
1100 __PACKAGE__->meta->make_immutable;
1106 =item * Think about making Relationship objects again