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, repetition, transposition. The first three 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 $options->{'type'} !~ /^(spelling|orthographic|grammatical|meaning|lexical|repetition|transposition)$/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. Uses GraphViz to do
378 this, because Graph::Easy doesn\'t cope well with long graphs. Unless
379 $recalculate is passed (and is a true value), the method will return a
380 cached copy of the SVG after the first call to the method.
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 $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
444 $edge->[0], $edge->[1], $varopts );
451 my( $self, @edge ) = @_;
452 # If edge is an arrayref, cope.
453 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
457 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
461 sub path_display_label {
462 my( $self, $edge ) = @_;
463 my @wits = $self->path_witnesses( $edge );
464 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
465 if( scalar @wits > $maj ) {
468 return join( ', ', @wits );
475 print $graph->as_graphml( $recalculate )
477 Returns a GraphML representation of the collation graph, with
478 transposition information and position information. Unless
479 $recalculate is passed (and is a true value), the method will return a
480 cached copy of the SVG after the first call to the method.
488 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
489 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
490 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
491 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
493 # Create the document and root node
494 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
495 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
496 $graphml->setDocumentElement( $root );
497 $root->setNamespace( $xsi_ns, 'xsi', 0 );
498 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
500 # Add the data keys for the graph
503 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
504 foreach my $datum ( @graph_attributes ) {
505 $graph_data_keys{$datum} = 'dg'.$gdi++;
506 my $key = $root->addNewChild( $graphml_ns, 'key' );
507 $key->setAttribute( 'attr.name', $datum );
508 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
509 $key->setAttribute( 'for', 'graph' );
510 $key->setAttribute( 'id', $graph_data_keys{$datum} );
513 # Add the data keys for nodes
520 is_start => 'boolean',
522 is_lacuna => 'boolean',
524 foreach my $datum ( keys %node_data ) {
525 $node_data_keys{$datum} = 'dn'.$ndi++;
526 my $key = $root->addNewChild( $graphml_ns, 'key' );
527 $key->setAttribute( 'attr.name', $datum );
528 $key->setAttribute( 'attr.type', $node_data{$datum} );
529 $key->setAttribute( 'for', 'node' );
530 $key->setAttribute( 'id', $node_data_keys{$datum} );
533 # Add the data keys for edges, i.e. witnesses
537 class => 'string', # Path or relationship?
538 witness => 'string', # ID/label for a path
539 relationship => 'string', # ID/label for a relationship
540 extra => 'boolean', # Path key
541 colocated => 'boolean', # Relationship key
542 non_correctable => 'boolean', # Relationship key
543 non_independent => 'boolean', # Relationship key
545 foreach my $datum ( keys %edge_data ) {
546 $edge_data_keys{$datum} = 'de'.$edi++;
547 my $key = $root->addNewChild( $graphml_ns, 'key' );
548 $key->setAttribute( 'attr.name', $datum );
549 $key->setAttribute( 'attr.type', $edge_data{$datum} );
550 $key->setAttribute( 'for', 'edge' );
551 $key->setAttribute( 'id', $edge_data_keys{$datum} );
554 # Add the collation graph itself
555 my $graph = $root->addNewChild( $graphml_ns, 'graph' );
556 $graph->setAttribute( 'edgedefault', 'directed' );
557 $graph->setAttribute( 'id', $self->tradition->name );
558 $graph->setAttribute( 'parse.edgeids', 'canonical' );
559 $graph->setAttribute( 'parse.edges', scalar($self->paths) );
560 $graph->setAttribute( 'parse.nodeids', 'canonical' );
561 $graph->setAttribute( 'parse.nodes', scalar($self->readings) );
562 $graph->setAttribute( 'parse.order', 'nodesfirst' );
564 # Collation attribute data
565 foreach my $datum ( @graph_attributes ) {
566 my $value = $datum eq 'version' ? '2.0' : $self->$datum;
567 _add_graphml_data( $graph, $graph_data_keys{$datum}, $value );
572 # Add our readings to the graph
573 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
574 my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
575 my $node_xmlid = 'n' . $node_ctr++;
576 $node_hash{ $n->id } = $node_xmlid;
577 $node_el->setAttribute( 'id', $node_xmlid );
578 foreach my $d ( keys %node_data ) {
580 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
587 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
588 # We add an edge in the graphml for every witness in $e.
589 foreach my $wit ( $self->path_witnesses( $e ) ) {
590 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
591 $node_hash{ $e->[0] },
592 $node_hash{ $e->[1] } );
593 my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
594 $edge_el->setAttribute( 'source', $from );
595 $edge_el->setAttribute( 'target', $to );
596 $edge_el->setAttribute( 'id', $id );
598 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
600 # It's a witness path, so add the witness
602 my $key = $edge_data_keys{'witness'};
603 # Is this an ante-corr witness?
604 my $aclabel = $self->ac_label;
605 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
606 # Keep the base witness
608 # ...and record that this is an 'extra' reading path
609 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
611 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
615 # Add the relationship edges
616 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->relationships ) {
617 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
618 $node_hash{ $e->[0] },
619 $node_hash{ $e->[1] } );
620 my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
621 $edge_el->setAttribute( 'source', $from );
622 $edge_el->setAttribute( 'target', $to );
623 $edge_el->setAttribute( 'id', $id );
625 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'relationship' );
627 my $data = $self->relations->get_edge_attributes( @$e );
628 # It's a relationship, so save the relationship data
629 _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $data->{type} );
630 _add_graphml_data( $edge_el, $edge_data_keys{'colocated'}, $data->{colocated} );
631 if( exists $data->{non_correctable} ) {
632 _add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'},
633 $data->{non_correctable} );
635 if( exists $data->{non_independent} ) {
636 _add_graphml_data( $edge_el, $edge_data_keys{'non_independent'},
637 $data->{non_independent} );
641 # Save and return the thing
642 my $result = decode_utf8( $graphml->toString(1) );
646 sub _add_graphml_data {
647 my( $el, $key, $value ) = @_;
648 return unless defined $value;
649 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
650 $data_el->setAttribute( 'key', $key );
651 $data_el->appendText( $value );
656 print $graph->as_csv( $recalculate )
658 Returns a CSV alignment table representation of the collation graph, one
659 row per witness (or witness uncorrected.) Unless $recalculate is passed
660 (and is a true value), the method will return a cached copy of the CSV
661 after the first call to the method.
667 my $table = $self->make_alignment_table;
668 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
670 foreach my $row ( @$table ) {
671 $csv->combine( @$row );
672 push( @result, decode_utf8( $csv->string ) );
674 return join( "\n", @result );
677 # Make an alignment table - $noderefs controls whether the objects
678 # in the table are the nodes or simply their readings.
680 sub make_alignment_table {
681 my( $self, $noderefs, $include ) = @_;
682 unless( $self->linear ) {
683 warn "Need a linear graph in order to make an alignment table";
688 my @all_pos = ( 1 .. $self->end->rank - 1 );
689 foreach my $wit ( $self->tradition->witnesses ) {
690 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
691 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
692 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
693 unshift( @row, $wit->sigil );
694 push( @$table, \@row );
695 if( $wit->is_layered ) {
696 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
697 $wit->sigil.$self->ac_label, $wit->sigil );
698 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
699 unshift( @ac_row, $wit->sigil . $self->ac_label );
700 push( @$table, \@ac_row );
706 # Winnow out the rows for any witness not included.
707 foreach my $row ( @$table ) {
708 next unless $include->{$row->[0]};
709 push( @$winnowed, $row );
714 # Return a table where the witnesses read in columns rather than rows.
715 my $turned = _turn_table( $table );
716 # TODO We should really go through and delete empty rows.
720 sub _make_witness_row {
721 my( $path, $positions, $noderefs ) = @_;
723 map { $char_hash{$_} = undef } @$positions;
724 foreach my $rdg ( @$path ) {
725 my $rtext = $rdg->text;
726 $rtext = '#LACUNA#' if $rdg->is_lacuna;
727 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
728 $char_hash{$rdg->rank} = $noderefs ? $rdg : $rtext;
730 my @row = map { $char_hash{$_} } @$positions;
731 # Fill in lacuna markers for undef spots in the row
732 my $last_el = shift @row;
733 my @filled_row = ( $last_el );
734 foreach my $el ( @row ) {
735 # If we are using node reference, make the lacuna node appear many times
736 # in the table. If not, use the lacuna tag.
737 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
738 $el = $noderefs ? $last_el : '#LACUNA#';
740 push( @filled_row, $el );
746 # Tiny utility function to say if a table element is a lacuna
749 return 1 if $el eq '#LACUNA#';
750 return 1 if ref( $el ) eq 'Text::Tradition::Collation::Reading'
755 # Helper to turn the witnesses along columns rather than rows. Assumes
760 return $result unless scalar @$table;
761 my $nrows = scalar @{$table->[0]};
762 foreach my $idx ( 0 .. $nrows - 1 ) {
763 foreach my $wit ( 0 .. $#{$table} ) {
764 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
772 =head2 Navigation methods
778 my $beginning = $collation->start();
780 Returns the beginning of the collation, a meta-reading with label '#START#'.
784 my $end = $collation->end();
786 Returns the end of the collation, a meta-reading with label '#END#'.
789 =item B<reading_sequence>
791 my @readings = $graph->reading_sequence( $first, $last, $path[, $alt_path] );
793 Returns the ordered list of readings, starting with $first and ending
794 with $last, along the given witness path. If no path is specified,
795 assume that the path is that of the base text (if any.)
799 # TODO Think about returning some lazy-eval iterator.
801 sub reading_sequence {
802 my( $self, $start, $end, $witness, $backup ) = @_;
804 $witness = $self->baselabel unless $witness;
805 my @readings = ( $start );
808 while( $n && $n->id ne $end->id ) {
809 if( exists( $seen{$n->id} ) ) {
810 warn "Detected loop at " . $n->id;
815 my $next = $self->next_reading( $n, $witness, $backup );
817 warn "Did not find any path for $witness from reading " . $n->id;
820 push( @readings, $next );
823 # Check that the last reading is our end reading.
824 my $last = $readings[$#readings];
825 warn "Last reading found from " . $start->text .
826 " for witness $witness is not the end!"
827 unless $last->id eq $end->id;
832 =item B<next_reading>
834 my $next_reading = $graph->next_reading( $reading, $witpath );
836 Returns the reading that follows the given reading along the given witness
842 # Return the successor via the corresponding path.
844 my $answer = $self->_find_linked_reading( 'next', @_ );
845 return $self->reading( $answer );
848 =item B<prior_reading>
850 my $prior_reading = $graph->prior_reading( $reading, $witpath );
852 Returns the reading that precedes the given reading along the given witness
858 # Return the predecessor via the corresponding path.
860 my $answer = $self->_find_linked_reading( 'prior', @_ );
861 return $self->reading( $answer );
864 sub _find_linked_reading {
865 my( $self, $direction, $node, $path, $alt_path ) = @_;
866 my @linked_paths = $direction eq 'next'
867 ? $self->sequence->edges_from( $node )
868 : $self->sequence->edges_to( $node );
869 return undef unless scalar( @linked_paths );
871 # We have to find the linked path that contains all of the
872 # witnesses supplied in $path.
873 my( @path_wits, @alt_path_wits );
874 @path_wits = sort( $self->witnesses_of_label( $path ) ) if $path;
875 @alt_path_wits = sort( $self->witnesses_of_label( $alt_path ) ) if $alt_path;
878 foreach my $le ( @linked_paths ) {
879 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
882 my @le_wits = $self->path_witnesses( $le );
883 if( _is_within( \@path_wits, \@le_wits ) ) {
884 # This is the right path.
885 return $direction eq 'next' ? $le->[1] : $le->[0];
886 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
890 # Got this far? Return the alternate path if it exists.
891 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
894 # Got this far? Return the base path if it exists.
895 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
898 # Got this far? We have no appropriate path.
899 warn "Could not find $direction node from " . $node->label
900 . " along path $path";
906 my( $set1, $set2 ) = @_;
907 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
908 foreach my $el ( @$set1 ) {
909 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
915 ## INITIALIZATION METHODS - for use by parsers
917 # For use when a collation is constructed from a base text and an apparatus.
918 # We have the sequences of readings and just need to add path edges.
919 # When we are done, clear out the witness path attributes, as they are no
921 # TODO Find a way to replace the witness path attributes with encapsulated functions?
923 sub make_witness_paths {
925 foreach my $wit ( $self->tradition->witnesses ) {
926 print STDERR "Making path for " . $wit->sigil . "\n";
927 $self->make_witness_path( $wit );
931 sub make_witness_path {
932 my( $self, $wit ) = @_;
933 my @chain = @{$wit->path};
934 my $sig = $wit->sigil;
935 foreach my $idx ( 0 .. $#chain-1 ) {
936 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
938 if( $wit->is_layered ) {
939 @chain = @{$wit->uncorrected_path};
940 foreach my $idx( 0 .. $#chain-1 ) {
941 my $source = $chain[$idx];
942 my $target = $chain[$idx+1];
943 $self->add_path( $source, $target, $sig.$self->ac_label )
944 unless $self->has_path( $source, $target, $sig );
948 $wit->clear_uncorrected_path;
951 sub calculate_ranks {
953 # Walk a version of the graph where every node linked by a relationship
954 # edge is fundamentally the same node, and do a topological ranking on
955 # the nodes in this graph.
956 my $topo_graph = Graph->new();
960 foreach my $r ( $self->readings ) {
961 next if exists $rel_containers{$r->id};
962 my @rels = $r->related_readings( 'colocated' );
964 # Make a relationship container.
966 my $rn = 'rel_container_' . $rel_ctr++;
967 $topo_graph->add_vertex( $rn );
969 $rel_containers{$_->id} = $rn;
972 # Add a new node to mirror the old node.
973 $rel_containers{$r->id} = $r->id;
974 $topo_graph->add_vertex( $r->id );
979 foreach my $r ( $self->readings ) {
980 foreach my $n ( $self->sequence->successors( $r->id ) ) {
981 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
982 $rel_containers{$n} );
983 $DB::single = 1 unless $tfrom && $tto;
984 $topo_graph->add_edge( $tfrom, $tto );
988 # Now do the rankings, starting with the start node.
989 my $topo_start = $rel_containers{$self->start->id};
990 my $node_ranks = { $topo_start => 0 };
991 my @curr_origin = ( $topo_start );
992 # A little iterative function.
993 while( @curr_origin ) {
994 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
996 # Transfer our rankings from the topological graph to the real one.
997 foreach my $r ( $self->readings ) {
998 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
999 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1002 die "No rank calculated for node " . $r->id
1003 . " - do you have a cycle in the graph?";
1009 my( $graph, $node_ranks, @current_nodes ) = @_;
1010 # Look at each of the children of @current_nodes. If all the child's
1011 # parents have a rank, assign it the highest rank + 1 and add it to
1012 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1013 # parent gets a rank.
1015 foreach my $c ( @current_nodes ) {
1016 warn "Current reading $c has no rank!"
1017 unless exists $node_ranks->{$c};
1018 # print STDERR "Looking at child of node $c, rank "
1019 # . $node_ranks->{$c} . "\n";
1020 foreach my $child ( $graph->successors( $c ) ) {
1021 next if exists $node_ranks->{$child};
1022 my $highest_rank = -1;
1024 foreach my $parent ( $graph->predecessors( $child ) ) {
1025 if( exists $node_ranks->{$parent} ) {
1026 $highest_rank = $node_ranks->{$parent}
1027 if $highest_rank <= $node_ranks->{$parent};
1034 my $c_rank = $highest_rank + 1;
1035 # print STDERR "Assigning rank $c_rank to node $child \n";
1036 $node_ranks->{$child} = $c_rank;
1037 push( @next_nodes, $child );
1043 # Another method to make up for rough collation methods. If the same reading
1044 # appears multiple times at the same rank, collapse the nodes.
1047 my %unique_rank_rdg;
1048 foreach my $rdg ( $self->readings ) {
1049 next unless $rdg->has_rank;
1050 my $key = $rdg->rank . "||" . $rdg->text;
1051 if( exists $unique_rank_rdg{$key} ) {
1053 print STDERR "Combining readings at same rank: $key\n";
1054 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1056 $unique_rank_rdg{$key} = $rdg;
1062 ## Utility functions
1064 # Return the string that joins together a list of witnesses for
1065 # display on a single path.
1066 sub witnesses_of_label {
1067 my( $self, $label ) = @_;
1068 my $regex = $self->wit_list_separator;
1069 my @answer = split( /\Q$regex\E/, $label );
1074 __PACKAGE__->meta->make_immutable;
1080 =item * Rationalize edge classes
1082 =item * Port the internal graph from Graph::Easy to Graph