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".
344 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
345 my $wits = $self->sequence->get_edge_attributes( @$e );
346 @all_witnesses{ keys %$wits } = 1;
348 return keys %all_witnesses;
351 sub related_readings {
352 my( $self, $reading, $colocated ) = @_;
354 if( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
355 $reading = $reading->id;
357 # print STDERR "Returning related objects\n";
359 # print STDERR "Returning related object names\n";
361 my @related = $self->relations->all_reachable( $reading );
363 my @colo = grep { $self->relations->has_edge_attribute( $reading, $_, 'colocated' ) } @related;
366 return $return_object ? map { $self->reading( $_ ) } @related : @related;
369 =head2 Output method(s)
375 print $graph->as_svg( $recalculate );
377 Returns an SVG string that represents the graph, via as_dot and graphviz.
384 my @cmd = qw/dot -Tsvg/;
386 my $dotfile = File::Temp->new();
388 # $dotfile->unlink_on_destroy(0);
389 binmode $dotfile, ':utf8';
390 print $dotfile $self->as_dot();
391 push( @cmd, $dotfile->filename );
392 run( \@cmd, ">", binary(), \$svg );
393 $svg = decode_utf8( $svg );
399 print $graph->as_dot( $view, $recalculate );
401 Returns a string that is the collation graph expressed in dot
402 (i.e. GraphViz) format. The 'view' argument determines what kind of
404 * 'path': a graph of witness paths through the collation (DEFAULT)
405 * 'relationship': a graph of how collation readings relate to
411 my( $self, $view ) = @_;
412 $view = 'sequence' unless $view;
413 # TODO consider making some of these things configurable
414 my $graph_name = $self->tradition->name;
415 $graph_name =~ s/[^\w\s]//g;
416 $graph_name = join( '_', split( /\s+/, $graph_name ) );
417 my $dot = sprintf( "digraph %s {\n", $graph_name );
418 $dot .= "\tedge [ arrowhead=open ];\n";
419 $dot .= "\tgraph [ rankdir=LR ];\n";
420 $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
421 11, "white", "filled", "ellipse" );
423 foreach my $reading ( $self->readings ) {
424 # Need not output nodes without separate labels
425 next if $reading->id eq $reading->text;
426 my $label = $reading->text;
427 $label =~ s/\"/\\\"/g;
428 $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
431 # TODO do something sensible for relationships
433 my @edges = $self->paths;
434 foreach my $edge ( @edges ) {
435 my %variables = ( 'color' => '#000000',
436 'fontcolor' => '#000000',
437 'label' => join( ', ', $self->path_display_label( $edge ) ),
439 my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
440 $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
441 $edge->[0], $edge->[1], $varopts );
448 my( $self, @edge ) = @_;
449 # If edge is an arrayref, cope.
450 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
454 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
458 sub path_display_label {
459 my( $self, $edge ) = @_;
460 my @wits = $self->path_witnesses( $edge );
461 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
462 if( scalar @wits > $maj ) {
465 return join( ', ', @wits );
472 print $graph->as_graphml( $recalculate )
474 Returns a GraphML representation of the collation graph, with
475 transposition information and position information. Unless
476 $recalculate is passed (and is a true value), the method will return a
477 cached copy of the SVG after the first call to the method.
485 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
486 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
487 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
488 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
490 # Create the document and root node
491 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
492 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
493 $graphml->setDocumentElement( $root );
494 $root->setNamespace( $xsi_ns, 'xsi', 0 );
495 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
497 # Add the data keys for the graph
500 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
501 foreach my $datum ( @graph_attributes ) {
502 $graph_data_keys{$datum} = 'dg'.$gdi++;
503 my $key = $root->addNewChild( $graphml_ns, 'key' );
504 $key->setAttribute( 'attr.name', $datum );
505 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
506 $key->setAttribute( 'for', 'graph' );
507 $key->setAttribute( 'id', $graph_data_keys{$datum} );
510 # Add the data keys for nodes
517 is_start => 'boolean',
519 is_lacuna => 'boolean',
521 foreach my $datum ( keys %node_data ) {
522 $node_data_keys{$datum} = 'dn'.$ndi++;
523 my $key = $root->addNewChild( $graphml_ns, 'key' );
524 $key->setAttribute( 'attr.name', $datum );
525 $key->setAttribute( 'attr.type', $node_data{$datum} );
526 $key->setAttribute( 'for', 'node' );
527 $key->setAttribute( 'id', $node_data_keys{$datum} );
530 # Add the data keys for edges, i.e. witnesses
534 witness => 'string', # ID/label for a path
535 relationship => 'string', # ID/label for a relationship
536 extra => 'boolean', # Path key
537 colocated => 'boolean', # Relationship key
538 non_correctable => 'boolean', # Relationship key
539 non_independent => 'boolean', # Relationship key
541 foreach my $datum ( keys %edge_data ) {
542 $edge_data_keys{$datum} = 'de'.$edi++;
543 my $key = $root->addNewChild( $graphml_ns, 'key' );
544 $key->setAttribute( 'attr.name', $datum );
545 $key->setAttribute( 'attr.type', $edge_data{$datum} );
546 $key->setAttribute( 'for', 'edge' );
547 $key->setAttribute( 'id', $edge_data_keys{$datum} );
550 # Add the collation graphs themselves
551 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
552 $sgraph->setAttribute( 'edgedefault', 'directed' );
553 $sgraph->setAttribute( 'id', $self->tradition->name );
554 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
555 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
556 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
557 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
558 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
560 my $rgraph = $root->addNewChild( $graphml_ns, 'graph' );
561 $rgraph->setAttribute( 'edgedefault', 'undirected' );
562 $rgraph->setAttribute( 'id', 'relationships' );
563 $rgraph->setAttribute( 'parse.edgeids', 'canonical' );
564 $rgraph->setAttribute( 'parse.edges', scalar($self->relationships) );
565 $rgraph->setAttribute( 'parse.nodeids', 'canonical' );
566 $rgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
567 $rgraph->setAttribute( 'parse.order', 'nodesfirst' );
569 # Collation attribute data
570 foreach my $datum ( @graph_attributes ) {
571 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
572 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
577 # Add our readings to the graphs
578 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
579 # Add to the main graph
580 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
581 my $node_xmlid = 'n' . $node_ctr++;
582 $node_hash{ $n->id } = $node_xmlid;
583 $node_el->setAttribute( 'id', $node_xmlid );
584 foreach my $d ( keys %node_data ) {
586 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
589 # Add to the relationships graph
590 my $rnode_el = $rgraph->addNewChild( $graphml_ns, 'node' );
591 $rnode_el->setAttribute( 'id', $node_xmlid );
594 # Add the path edges to the sequence graph
596 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
597 # We add an edge in the graphml for every witness in $e.
598 foreach my $wit ( $self->path_witnesses( $e ) ) {
599 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
600 $node_hash{ $e->[0] },
601 $node_hash{ $e->[1] } );
602 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
603 $edge_el->setAttribute( 'source', $from );
604 $edge_el->setAttribute( 'target', $to );
605 $edge_el->setAttribute( 'id', $id );
607 # It's a witness path, so add the witness
609 my $key = $edge_data_keys{'witness'};
610 # Is this an ante-corr witness?
611 my $aclabel = $self->ac_label;
612 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
613 # Keep the base witness
615 # ...and record that this is an 'extra' reading path
616 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
618 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
622 # Add the relationship edges to the relationships graph
623 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->relationships ) {
624 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
625 $node_hash{ $e->[0] },
626 $node_hash{ $e->[1] } );
627 my $edge_el = $rgraph->addNewChild( $graphml_ns, 'edge' );
628 $edge_el->setAttribute( 'source', $from );
629 $edge_el->setAttribute( 'target', $to );
630 $edge_el->setAttribute( 'id', $id );
632 my $data = $self->relations->get_edge_attributes( @$e );
633 # It's a relationship, so save the relationship data
634 _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $data->{type} );
635 _add_graphml_data( $edge_el, $edge_data_keys{'colocated'}, $data->{colocated} );
636 if( exists $data->{non_correctable} ) {
637 _add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'},
638 $data->{non_correctable} );
640 if( exists $data->{non_independent} ) {
641 _add_graphml_data( $edge_el, $edge_data_keys{'non_independent'},
642 $data->{non_independent} );
646 # Save and return the thing
647 my $result = decode_utf8( $graphml->toString(1) );
651 sub _add_graphml_data {
652 my( $el, $key, $value ) = @_;
653 return unless defined $value;
654 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
655 $data_el->setAttribute( 'key', $key );
656 $data_el->appendText( $value );
661 print $graph->as_csv( $recalculate )
663 Returns a CSV alignment table representation of the collation graph, one
664 row per witness (or witness uncorrected.)
670 my $table = $self->make_alignment_table;
671 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
673 # Make the header row
674 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
675 push( @result, decode_utf8( $csv->string ) );
676 # Make the rest of the rows
677 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
678 my @rowobjs = map { $_->[$idx] } @{$table->{'alignment'}};
679 my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
680 $csv->combine( @row );
681 push( @result, decode_utf8( $csv->string ) );
683 return join( "\n", @result );
686 =item B<make_alignment_table>
688 my $table = $graph->make_alignment_table( $use_refs, \@wits_to_include )
690 Return a reference to an alignment table, in the format described at
691 L<http://gregor.middell.net/collatex>. If $use_refs is set to 1, the reading
692 object is returned in the table; if not, the text of the reading is returned.
693 If $wits_to_include is set to an arrayref, only the witnesses listed will be
694 included in the table.
698 sub make_alignment_table {
699 my( $self, $noderefs, $include ) = @_;
700 unless( $self->linear ) {
701 warn "Need a linear graph in order to make an alignment table";
704 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
705 my @all_pos = ( 1 .. $self->end->rank - 1 );
706 foreach my $wit ( $self->tradition->witnesses ) {
708 next unless grep { $_ eq $wit->sigil } @$include;
710 $DB::single = 1 if $wit->sigil eq 'U';
711 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
712 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
713 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
714 push( @{$table->{'alignment'}},
715 { 'witness' => $wit->sigil, 'tokens' => \@row } );
716 if( $wit->is_layered ) {
717 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
718 $wit->sigil.$self->ac_label, $wit->sigil );
719 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
720 push( @{$table->{'alignment'}},
721 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
727 sub _make_witness_row {
728 my( $path, $positions, $noderefs ) = @_;
730 map { $char_hash{$_} = undef } @$positions;
732 foreach my $rdg ( @$path ) {
733 my $rtext = $rdg->text;
734 $rtext = '#LACUNA#' if $rdg->is_lacuna;
735 print STDERR "rank " . $rdg->rank . "\n" if $debug;
736 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
737 $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
740 my @row = map { $char_hash{$_} } @$positions;
741 # Fill in lacuna markers for undef spots in the row
742 my $last_el = shift @row;
743 my @filled_row = ( $last_el );
744 foreach my $el ( @row ) {
745 # If we are using node reference, make the lacuna node appear many times
746 # in the table. If not, use the lacuna tag.
747 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
748 $el = $noderefs ? { 't' => $last_el } : { 't' => '#LACUNA#' };
750 push( @filled_row, $el );
756 # Tiny utility function to say if a table element is a lacuna
759 return 1 if $el->{'t'} eq '#LACUNA#';
760 return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
761 && $el->{'t'}->is_lacuna;
765 # Helper to turn the witnesses along columns rather than rows. Assumes
770 return $result unless scalar @$table;
771 my $nrows = scalar @{$table->[0]};
772 foreach my $idx ( 0 .. $nrows - 1 ) {
773 foreach my $wit ( 0 .. $#{$table} ) {
774 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
782 =head2 Navigation methods
788 my $beginning = $collation->start();
790 Returns the beginning of the collation, a meta-reading with label '#START#'.
794 my $end = $collation->end();
796 Returns the end of the collation, a meta-reading with label '#END#'.
799 =item B<reading_sequence>
801 my @readings = $graph->reading_sequence( $first, $last, $path[, $alt_path] );
803 Returns the ordered list of readings, starting with $first and ending
804 with $last, along the given witness path. If no path is specified,
805 assume that the path is that of the base text (if any.)
809 # TODO Think about returning some lazy-eval iterator.
811 sub reading_sequence {
812 my( $self, $start, $end, $witness, $backup ) = @_;
814 $witness = $self->baselabel unless $witness;
815 my @readings = ( $start );
818 while( $n && $n->id ne $end->id ) {
819 if( exists( $seen{$n->id} ) ) {
820 warn "Detected loop at " . $n->id;
825 my $next = $self->next_reading( $n, $witness, $backup );
827 warn "Did not find any path for $witness from reading " . $n->id;
830 push( @readings, $next );
833 # Check that the last reading is our end reading.
834 my $last = $readings[$#readings];
835 warn "Last reading found from " . $start->text .
836 " for witness $witness is not the end!"
837 unless $last->id eq $end->id;
842 =item B<next_reading>
844 my $next_reading = $graph->next_reading( $reading, $witpath );
846 Returns the reading that follows the given reading along the given witness
852 # Return the successor via the corresponding path.
854 my $answer = $self->_find_linked_reading( 'next', @_ );
855 return undef unless $answer;
856 return $self->reading( $answer );
859 =item B<prior_reading>
861 my $prior_reading = $graph->prior_reading( $reading, $witpath );
863 Returns the reading that precedes the given reading along the given witness
869 # Return the predecessor via the corresponding path.
871 my $answer = $self->_find_linked_reading( 'prior', @_ );
872 return $self->reading( $answer );
875 sub _find_linked_reading {
876 my( $self, $direction, $node, $path, $alt_path ) = @_;
877 my @linked_paths = $direction eq 'next'
878 ? $self->sequence->edges_from( $node )
879 : $self->sequence->edges_to( $node );
880 return undef unless scalar( @linked_paths );
882 # We have to find the linked path that contains all of the
883 # witnesses supplied in $path.
884 my( @path_wits, @alt_path_wits );
885 @path_wits = sort( $self->witnesses_of_label( $path ) ) if $path;
886 @alt_path_wits = sort( $self->witnesses_of_label( $alt_path ) ) if $alt_path;
889 foreach my $le ( @linked_paths ) {
890 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
893 my @le_wits = $self->path_witnesses( $le );
894 if( _is_within( \@path_wits, \@le_wits ) ) {
895 # This is the right path.
896 return $direction eq 'next' ? $le->[1] : $le->[0];
897 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
901 # Got this far? Return the alternate path if it exists.
902 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
905 # Got this far? Return the base path if it exists.
906 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
909 # Got this far? We have no appropriate path.
910 warn "Could not find $direction node from " . $node->id
911 . " along path $path";
917 my( $set1, $set2 ) = @_;
918 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
919 foreach my $el ( @$set1 ) {
920 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
926 ## INITIALIZATION METHODS - for use by parsers
928 # For use when a collation is constructed from a base text and an apparatus.
929 # We have the sequences of readings and just need to add path edges.
930 # When we are done, clear out the witness path attributes, as they are no
932 # TODO Find a way to replace the witness path attributes with encapsulated functions?
934 sub make_witness_paths {
936 foreach my $wit ( $self->tradition->witnesses ) {
937 # print STDERR "Making path for " . $wit->sigil . "\n";
938 $self->make_witness_path( $wit );
942 sub make_witness_path {
943 my( $self, $wit ) = @_;
944 my @chain = @{$wit->path};
945 my $sig = $wit->sigil;
946 foreach my $idx ( 0 .. $#chain-1 ) {
947 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
949 if( $wit->is_layered ) {
950 @chain = @{$wit->uncorrected_path};
951 foreach my $idx( 0 .. $#chain-1 ) {
952 my $source = $chain[$idx];
953 my $target = $chain[$idx+1];
954 $self->add_path( $source, $target, $sig.$self->ac_label )
955 unless $self->has_path( $source, $target, $sig );
959 $wit->clear_uncorrected_path;
962 sub calculate_ranks {
964 # Walk a version of the graph where every node linked by a relationship
965 # edge is fundamentally the same node, and do a topological ranking on
966 # the nodes in this graph.
967 my $topo_graph = Graph->new();
971 foreach my $r ( $self->readings ) {
972 next if exists $rel_containers{$r->id};
973 my @rels = $r->related_readings( 'colocated' );
975 # Make a relationship container.
977 my $rn = 'rel_container_' . $rel_ctr++;
978 $topo_graph->add_vertex( $rn );
980 $rel_containers{$_->id} = $rn;
983 # Add a new node to mirror the old node.
984 $rel_containers{$r->id} = $r->id;
985 $topo_graph->add_vertex( $r->id );
990 foreach my $r ( $self->readings ) {
991 foreach my $n ( $self->sequence->successors( $r->id ) ) {
992 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
993 $rel_containers{$n} );
994 $DB::single = 1 unless $tfrom && $tto;
995 $topo_graph->add_edge( $tfrom, $tto );
999 # Now do the rankings, starting with the start node.
1000 my $topo_start = $rel_containers{$self->start->id};
1001 my $node_ranks = { $topo_start => 0 };
1002 my @curr_origin = ( $topo_start );
1003 # A little iterative function.
1004 while( @curr_origin ) {
1005 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1007 # Transfer our rankings from the topological graph to the real one.
1008 foreach my $r ( $self->readings ) {
1009 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1010 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1013 die "No rank calculated for node " . $r->id
1014 . " - do you have a cycle in the graph?";
1020 my( $graph, $node_ranks, @current_nodes ) = @_;
1021 # Look at each of the children of @current_nodes. If all the child's
1022 # parents have a rank, assign it the highest rank + 1 and add it to
1023 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1024 # parent gets a rank.
1026 foreach my $c ( @current_nodes ) {
1027 warn "Current reading $c has no rank!"
1028 unless exists $node_ranks->{$c};
1029 # print STDERR "Looking at child of node $c, rank "
1030 # . $node_ranks->{$c} . "\n";
1031 foreach my $child ( $graph->successors( $c ) ) {
1032 next if exists $node_ranks->{$child};
1033 my $highest_rank = -1;
1035 foreach my $parent ( $graph->predecessors( $child ) ) {
1036 if( exists $node_ranks->{$parent} ) {
1037 $highest_rank = $node_ranks->{$parent}
1038 if $highest_rank <= $node_ranks->{$parent};
1045 my $c_rank = $highest_rank + 1;
1046 # print STDERR "Assigning rank $c_rank to node $child \n";
1047 $node_ranks->{$child} = $c_rank;
1048 push( @next_nodes, $child );
1054 # Another method to make up for rough collation methods. If the same reading
1055 # appears multiple times at the same rank, collapse the nodes.
1058 my %unique_rank_rdg;
1059 foreach my $rdg ( $self->readings ) {
1060 next unless $rdg->has_rank;
1061 my $key = $rdg->rank . "||" . $rdg->text;
1062 if( exists $unique_rank_rdg{$key} ) {
1064 # print STDERR "Combining readings at same rank: $key\n";
1065 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1067 $unique_rank_rdg{$key} = $rdg;
1073 ## Utility functions
1075 # Return the string that joins together a list of witnesses for
1076 # display on a single path.
1077 sub witnesses_of_label {
1078 my( $self, $label ) = @_;
1079 my $regex = $self->wit_list_separator;
1080 my @answer = split( /\Q$regex\E/, $label );
1085 __PACKAGE__->meta->make_immutable;
1091 =item * Think about making Relationship objects again