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;
16 default => sub { Graph->new() },
24 isa => 'Text::Tradition::Collation::RelationshipStore',
26 relationships => 'relationships',
27 related_readings => 'related_readings',
29 writer => '_set_relations',
34 isa => 'Text::Tradition',
39 isa => 'HashRef[Text::Tradition::Collation::Reading]',
43 _add_reading => 'set',
44 del_reading => 'delete',
45 has_reading => 'exists',
48 default => sub { {} },
51 has 'wit_list_separator' => (
60 default => 'base text',
69 has 'collapse_punctuation' => (
83 isa => 'Text::Tradition::Collation::Reading',
84 writer => '_set_start',
90 isa => 'Text::Tradition::Collation::Reading',
97 Text::Tradition::Collation - a software model for a text collation
102 my $t = Text::Tradition->new(
103 'name' => 'this is a text',
105 'file' => '/path/to/tei_parallel_seg_file.xml' );
107 my $c = $t->collation;
108 my @readings = $c->readings;
109 my @paths = $c->paths;
110 my @relationships = $c->relationships;
112 my $svg_variant_graph = $t->collation->as_svg();
116 Text::Tradition is a library for representation and analysis of collated
117 texts, particularly medieval ones. The Collation is the central feature of
118 a Tradition, where the text, its sequence of readings, and its relationships
119 between readings are actually kept.
125 The constructor. Takes a hash or hashref of the following arguments:
129 =item * tradition - The Text::Tradition object to which the collation
132 =item * linear - Whether the collation should be linear; that is, whether
133 transposed readings should be treated as two linked readings rather than one,
134 and therefore whether the collation graph is acyclic. Defaults to true.
136 =item * collapse_punctuation - TODO
138 =item * baselabel - The default label for the path taken by a base text
139 (if any). Defaults to 'base text'.
141 =item * wit_list_separator - The string to join a list of witnesses for
142 purposes of making labels in display graphs. Defaults to ', '.
144 =item * ac_label - The extra label to tack onto a witness sigil when
145 representing another layer of path for the given witness - that is, when
146 a text has more than one possible reading due to scribal corrections or
147 the like. Defaults to ' (a.c.)'.
157 =head2 collapse_punctuation
159 =head2 wit_list_separator
165 Simple accessors for collation attributes.
169 The meta-reading at the start of every witness path.
173 The meta-reading at the end of every witness path.
177 Returns all Reading objects in the graph.
179 =head2 reading( $id )
181 Returns the Reading object corresponding to the given ID.
183 =head2 add_reading( $reading_args )
185 Adds a new reading object to the collation.
186 See L<Text::Tradition::Collation::Reading> for the available arguments.
188 =head2 del_reading( $object_or_id )
190 Removes the given reading from the collation, implicitly removing its
191 paths and relationships.
193 =head2 merge_readings( $main, $second )
195 Merges the $second reading into the $main one.
196 The arguments may be either readings or reading IDs.
198 =head2 has_reading( $id )
200 Predicate to see whether a given reading ID is in the graph.
202 =head2 reading_witnesses( $object_or_id )
204 Returns a list of sigils whose witnesses contain the reading.
208 Returns all reading paths within the document - that is, all edges in the
209 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
211 =head2 add_path( $source, $target, $sigil )
213 Links the given readings in the collation in sequence, under the given witness
214 sigil. The readings may be specified by object or ID.
216 =head2 del_path( $source, $target, $sigil )
218 Links the given readings in the collation in sequence, under the given witness
219 sigil. The readings may be specified by object or ID.
221 =head2 has_path( $source, $target );
223 Returns true if the two readings are linked in sequence in any witness.
224 The readings may be specified by object or ID.
228 Returns all Relationship objects in the collation.
230 =head2 add_relationship( $reading, $other_reading, $options )
232 Adds a new relationship of the type given in $options between the two readings,
233 which may be specified by object or ID. Returns a value of ( $status, @vectors)
234 where $status is true on success, and @vectors is a list of relationship edges
235 that were ultimately added.
236 See L<Text::Tradition::Collation::Relationship> for the available options.
242 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
243 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
244 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
247 ### Reading construct/destruct functions
250 my( $self, $reading ) = @_;
251 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
252 my %args = %$reading;
253 $reading = Text::Tradition::Collation::Reading->new(
254 'collation' => $self,
257 # First check to see if a reading with this ID exists.
258 if( $self->reading( $reading->id ) ) {
259 warn "Collation already has a reading with id " . $reading->id;
262 $self->_add_reading( $reading->id => $reading );
263 # Once the reading has been added, put it in both graphs.
264 $self->sequence->add_vertex( $reading->id );
265 $self->relations->add_reading( $reading->id );
269 around del_reading => sub {
274 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
277 # Remove the reading from the graphs.
278 $self->sequence->delete_vertex( $arg );
279 $self->relations->delete_reading( $arg );
282 $self->$orig( $arg );
285 # merge_readings( $main, $to_be_deleted );
290 # We only need the IDs for adding paths to the graph, not the reading
291 # objects themselves.
292 my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
294 # The kept reading should inherit the paths and the relationships
295 # of the deleted reading.
296 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
297 my @vector = ( $kept );
298 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
299 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
300 next if $vector[0] eq $vector[1]; # Don't add a self loop
301 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
302 $self->sequence->add_edge( @vector );
303 my $fwits = $self->sequence->get_edge_attributes( @vector );
304 @wits{keys %$fwits} = values %$fwits;
305 $self->sequence->set_edge_attributes( @vector, \%wits );
307 $self->relations->merge_readings( $kept, $deleted, $combine_char );
309 # Do the deletion deed.
310 if( $combine_char ) {
311 my $kept_obj = $self->reading( $kept );
312 my $new_text = join( $combine_char, $kept_obj->text,
313 $self->reading( $deleted )->text );
314 $kept_obj->alter_text( $new_text );
316 $self->del_reading( $deleted );
320 # Helper function for manipulating the graph.
321 sub _stringify_args {
322 my( $self, $first, $second, $arg ) = @_;
324 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
325 $second = $second->id
326 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
327 return( $first, $second, $arg );
330 # Helper function for manipulating the graph.
331 sub _objectify_args {
332 my( $self, $first, $second, $arg ) = @_;
333 $first = $self->reading( $first )
334 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
335 $second = $self->reading( $second )
336 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
337 return( $first, $second, $arg );
344 # We only need the IDs for adding paths to the graph, not the reading
345 # objects themselves.
346 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
348 # Connect the readings
349 $self->sequence->add_edge( $source, $target );
350 # Note the witness in question
351 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
357 if( ref( $_[0] ) eq 'ARRAY' ) {
364 # We only need the IDs for adding paths to the graph, not the reading
365 # objects themselves.
366 my( $source, $target, $wit ) = $self->_stringify_args( @args );
368 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
369 $self->sequence->delete_edge_attribute( $source, $target, $wit );
371 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
372 $self->sequence->delete_edge( $source, $target );
377 # Extra graph-alike utility
380 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
381 return undef unless $self->sequence->has_edge( $source, $target );
382 return $self->sequence->has_edge_attribute( $source, $target, $wit );
385 =head2 clear_witness( @sigil_list )
387 Clear the given witnesses out of the collation entirely, removing references
388 to them in paths, and removing readings that belong only to them. Should only
389 be called via $tradition->del_witness.
394 my( $self, @sigils ) = @_;
396 # Clear the witness(es) out of the paths
397 foreach my $e ( $self->paths ) {
398 foreach my $sig ( @sigils ) {
399 $self->del_path( $e, $sig );
403 # Clear out the newly unused readings
404 foreach my $r ( $self->readings ) {
405 unless( $self->reading_witnesses( $r ) ) {
406 $self->del_reading( $r );
411 sub add_relationship {
413 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
414 my( $ret, @vectors ) = $self->relations->add_relationship( $source,
415 $self->reading( $source ), $target, $self->reading( $target ), $opts );
416 # Force a full rank recalculation every time. Yuck.
417 $self->calculate_ranks() if $ret && $self->end->has_rank;
418 return( $ret, @vectors );
421 =head2 reading_witnesses( $reading )
423 Return a list of sigils corresponding to the witnesses in which the reading appears.
427 sub reading_witnesses {
428 my( $self, $reading ) = @_;
429 # We need only check either the incoming or the outgoing edges; I have
430 # arbitrarily chosen "incoming". Thus, special-case the start node.
431 if( $reading eq $self->start ) {
432 return map { $_->sigil } $self->tradition->witnesses;
435 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
436 my $wits = $self->sequence->get_edge_attributes( @$e );
437 @all_witnesses{ keys %$wits } = 1;
439 return keys %all_witnesses;
442 =head1 OUTPUT METHODS
446 Returns an SVG string that represents the graph, via as_dot and graphviz.
453 my @cmd = qw/dot -Tsvg/;
455 my $dotfile = File::Temp->new();
457 # $dotfile->unlink_on_destroy(0);
458 binmode $dotfile, ':utf8';
459 print $dotfile $self->as_dot();
460 push( @cmd, $dotfile->filename );
461 run( \@cmd, ">", binary(), \$svg );
462 $svg = decode_utf8( $svg );
466 =head2 svg_subgraph( $from, $to )
468 Returns an SVG string that represents the portion of the graph given by the
469 specified range. The $from and $to variables refer to ranks within the graph.
474 my( $self, $from, $to ) = @_;
476 my $dot = $self->as_dot( $from, $to );
478 warn "Could not output a graph with range $from - $to";
482 my @cmd = qw/dot -Tsvg/;
484 my $dotfile = File::Temp->new();
486 # $dotfile->unlink_on_destroy(0);
487 binmode $dotfile, ':utf8';
489 push( @cmd, $dotfile->filename );
490 run( \@cmd, ">", binary(), \$svg );
491 $svg = decode_utf8( $svg );
496 =head2 as_dot( $from, $to )
498 Returns a string that is the collation graph expressed in dot
499 (i.e. GraphViz) format. If $from or $to is passed, as_dot creates
500 a subgraph rather than the entire graph.
505 my( $self, $startrank, $endrank ) = @_;
507 # Check the arguments
509 return if $endrank && $startrank > $endrank;
510 return if $startrank > $self->end->rank;
512 if( defined $endrank ) {
513 return if $endrank < 0;
514 $endrank = undef if $endrank == $self->end->rank;
517 # TODO consider making some of these things configurable
518 my $graph_name = $self->tradition->name;
519 $graph_name =~ s/[^\w\s]//g;
520 $graph_name = join( '_', split( /\s+/, $graph_name ) );
521 my $dot = sprintf( "digraph %s {\n", $graph_name );
522 $dot .= "\tedge [ arrowhead=open ];\n";
523 $dot .= "\tgraph [ rankdir=LR,bgcolor=none ];\n";
524 $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
525 11, "white", "filled", "ellipse" );
527 # Output substitute start/end readings if necessary
529 $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
532 $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
534 my %used; # Keep track of the readings that actually appear in the graph
537 foreach my $reading ( $self->readings ) {
538 # Only output readings within our rank range.
539 next if $startrank && $reading->rank < $startrank;
540 next if $endrank && $reading->rank > $endrank;
541 $used{$reading->id} = 1;
542 $subedges{$reading->id} = '#SUBSTART#'
543 if $startrank && $startrank == $reading->rank;
544 $subedges{$reading->id} = '#SUBEND#'
545 if $endrank && $endrank == $reading->rank;
546 # Need not output nodes without separate labels
547 next if $reading->id eq $reading->text;
548 my $label = $reading->punctuated_form;
549 $label =~ s/\"/\\\"/g;
550 $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
553 # Add substitute start and end edges if necessary
554 foreach my $node ( keys %subedges ) {
555 my @vector = ( $subedges{$node}, $node );
556 @vector = reverse( @vector ) if $vector[0] =~ /END/;
557 my $witstr = join( ', ', sort $self->reading_witnesses( $self->reading( $node ) ) );
558 my %variables = ( 'color' => '#000000',
559 'fontcolor' => '#000000',
562 my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
563 $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n", @vector, $varopts );
567 my @edges = $self->paths;
568 foreach my $edge ( @edges ) {
569 # Do we need to output this edge?
570 if( $used{$edge->[0]} && $used{$edge->[1]} ) {;
571 my %variables = ( 'color' => '#000000',
572 'fontcolor' => '#000000',
573 'label' => join( ', ', $self->path_display_label( $edge ) ),
575 my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
576 # Account for the rank gap if necessary
577 my $rankgap = $self->reading( $edge->[1] )->rank
578 - $self->reading( $edge->[0] )->rank;
579 $varopts .= ", minlen=$rankgap" if $rankgap > 1;
580 $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
581 $edge->[0], $edge->[1], $varopts );
590 my( $self, @edge ) = @_;
591 # If edge is an arrayref, cope.
592 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
596 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
600 sub path_display_label {
601 my( $self, $edge ) = @_;
602 my @wits = $self->path_witnesses( $edge );
603 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
604 if( scalar @wits > $maj ) {
607 return join( ', ', @wits );
614 Returns a GraphML representation of the collation. The GraphML will contain
615 two graphs. The first expresses the attributes of the readings and the witness
616 paths that link them; the second expresses the relationships that link the
617 readings. This is the native transfer format for a tradition.
626 my $datafile = 't/data/florilegium_tei_ps.xml';
627 my $tradition = Text::Tradition->new( 'input' => 'TEI',
632 ok( $tradition, "Got a tradition object" );
633 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
634 ok( $tradition->collation, "Tradition has a collation" );
636 my $c = $tradition->collation;
637 is( scalar $c->readings, $READINGS, "Collation has all readings" );
638 is( scalar $c->paths, $PATHS, "Collation has all paths" );
639 is( scalar $c->relationships, 0, "Collation has all relationships" );
641 # Add a few relationships
642 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
643 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
644 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
646 # Now write it to GraphML and parse it again.
648 my $graphml = $c->as_graphml;
649 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
650 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
651 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
652 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
662 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
663 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
664 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
665 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
667 # Create the document and root node
668 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
669 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
670 $graphml->setDocumentElement( $root );
671 $root->setNamespace( $xsi_ns, 'xsi', 0 );
672 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
674 # Add the data keys for the graph
677 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
678 foreach my $datum ( @graph_attributes ) {
679 $graph_data_keys{$datum} = 'dg'.$gdi++;
680 my $key = $root->addNewChild( $graphml_ns, 'key' );
681 $key->setAttribute( 'attr.name', $datum );
682 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
683 $key->setAttribute( 'for', 'graph' );
684 $key->setAttribute( 'id', $graph_data_keys{$datum} );
687 # Add the data keys for nodes
694 is_start => 'boolean',
696 is_lacuna => 'boolean',
698 foreach my $datum ( keys %node_data ) {
699 $node_data_keys{$datum} = 'dn'.$ndi++;
700 my $key = $root->addNewChild( $graphml_ns, 'key' );
701 $key->setAttribute( 'attr.name', $datum );
702 $key->setAttribute( 'attr.type', $node_data{$datum} );
703 $key->setAttribute( 'for', 'node' );
704 $key->setAttribute( 'id', $node_data_keys{$datum} );
707 # Add the data keys for edges, i.e. witnesses
711 class => 'string', # Class, deprecated soon
712 witness => 'string', # ID/label for a path
713 relationship => 'string', # ID/label for a relationship
714 extra => 'boolean', # Path key
715 scope => 'string', # Relationship key
716 non_correctable => 'boolean', # Relationship key
717 non_independent => 'boolean', # Relationship key
719 foreach my $datum ( keys %edge_data ) {
720 $edge_data_keys{$datum} = 'de'.$edi++;
721 my $key = $root->addNewChild( $graphml_ns, 'key' );
722 $key->setAttribute( 'attr.name', $datum );
723 $key->setAttribute( 'attr.type', $edge_data{$datum} );
724 $key->setAttribute( 'for', 'edge' );
725 $key->setAttribute( 'id', $edge_data_keys{$datum} );
728 # Add the collation graph itself
729 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
730 $sgraph->setAttribute( 'edgedefault', 'directed' );
731 $sgraph->setAttribute( 'id', $self->tradition->name );
732 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
733 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
734 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
735 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
736 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
738 # Collation attribute data
739 foreach my $datum ( @graph_attributes ) {
740 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
741 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
746 # Add our readings to the graph
747 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
748 # Add to the main graph
749 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
750 my $node_xmlid = 'n' . $node_ctr++;
751 $node_hash{ $n->id } = $node_xmlid;
752 $node_el->setAttribute( 'id', $node_xmlid );
753 foreach my $d ( keys %node_data ) {
755 $nval = $n->punctuated_form if $d eq 'text';
756 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
761 # Add the path edges to the sequence graph
763 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
764 # We add an edge in the graphml for every witness in $e.
765 foreach my $wit ( $self->path_witnesses( $e ) ) {
766 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
767 $node_hash{ $e->[0] },
768 $node_hash{ $e->[1] } );
769 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
770 $edge_el->setAttribute( 'source', $from );
771 $edge_el->setAttribute( 'target', $to );
772 $edge_el->setAttribute( 'id', $id );
774 # It's a witness path, so add the witness
776 my $key = $edge_data_keys{'witness'};
777 # Is this an ante-corr witness?
778 my $aclabel = $self->ac_label;
779 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
780 # Keep the base witness
782 # ...and record that this is an 'extra' reading path
783 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
785 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
786 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
790 # Add the relationship graph to the XML
791 $self->relations->as_graphml( $graphml_ns, $root, \%node_hash,
792 $node_data_keys{'id'}, \%edge_data_keys );
794 # Save and return the thing
795 my $result = decode_utf8( $graphml->toString(1) );
799 sub _add_graphml_data {
800 my( $el, $key, $value ) = @_;
801 return unless defined $value;
802 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
803 $data_el->setAttribute( 'key', $key );
804 $data_el->appendText( $value );
809 Returns a CSV alignment table representation of the collation graph, one
810 row per witness (or witness uncorrected.)
816 my $table = $self->make_alignment_table;
817 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
819 # Make the header row
820 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
821 push( @result, decode_utf8( $csv->string ) );
822 # Make the rest of the rows
823 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
824 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
825 my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
826 $csv->combine( @row );
827 push( @result, decode_utf8( $csv->string ) );
829 return join( "\n", @result );
832 =head2 make_alignment_table( $use_refs, $include_witnesses )
834 Return a reference to an alignment table, in a slightly enhanced CollateX
835 format which looks like this:
837 $table = { alignment => [ { witness => "SIGIL",
838 tokens => [ { t => "TEXT" }, ... ] },
840 tokens => [ { t => "TEXT" }, ... ] },
844 If $use_refs is set to 1, the reading object is returned in the table
845 instead of READINGTEXT; if not, the text of the reading is returned.
847 If $include_witnesses is set to a hashref, only the witnesses whose sigil
848 keys have a true hash value will be included.
852 sub make_alignment_table {
853 my( $self, $noderefs, $include ) = @_;
854 unless( $self->linear ) {
855 warn "Need a linear graph in order to make an alignment table";
858 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
859 my @all_pos = ( 1 .. $self->end->rank - 1 );
860 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
862 next unless $include->{$wit->sigil};
864 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
865 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
866 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
867 push( @{$table->{'alignment'}},
868 { 'witness' => $wit->sigil, 'tokens' => \@row } );
869 if( $wit->is_layered ) {
870 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
871 $wit->sigil.$self->ac_label, $wit->sigil );
872 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
873 push( @{$table->{'alignment'}},
874 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
880 sub _make_witness_row {
881 my( $path, $positions, $noderefs ) = @_;
883 map { $char_hash{$_} = undef } @$positions;
885 foreach my $rdg ( @$path ) {
886 my $rtext = $rdg->text;
887 $rtext = '#LACUNA#' if $rdg->is_lacuna;
888 print STDERR "rank " . $rdg->rank . "\n" if $debug;
889 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
890 $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
893 my @row = map { $char_hash{$_} } @$positions;
894 # Fill in lacuna markers for undef spots in the row
895 my $last_el = shift @row;
896 my @filled_row = ( $last_el );
897 foreach my $el ( @row ) {
898 # If we are using node reference, make the lacuna node appear many times
899 # in the table. If not, use the lacuna tag.
900 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
901 $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
903 push( @filled_row, $el );
909 # Tiny utility function to say if a table element is a lacuna
912 return 1 if $el->{'t'} eq '#LACUNA#';
913 return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
914 && $el->{'t'}->is_lacuna;
918 # Helper to turn the witnesses along columns rather than rows. Assumes
923 return $result unless scalar @$table;
924 my $nrows = scalar @{$table->[0]};
925 foreach my $idx ( 0 .. $nrows - 1 ) {
926 foreach my $wit ( 0 .. $#{$table} ) {
927 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
933 =head1 NAVIGATION METHODS
935 =head2 reading_sequence( $first, $last, $sigil, $backup )
937 Returns the ordered list of readings, starting with $first and ending
938 with $last, for the witness given in $sigil. If a $backup sigil is
939 specified (e.g. when walking a layered witness), it will be used wherever
940 no $sigil path exists. If there is a base text reading, that will be
941 used wherever no path exists for $sigil or $backup.
945 # TODO Think about returning some lazy-eval iterator.
947 sub reading_sequence {
948 my( $self, $start, $end, $witness, $backup ) = @_;
950 $witness = $self->baselabel unless $witness;
951 my @readings = ( $start );
954 while( $n && $n->id ne $end->id ) {
955 if( exists( $seen{$n->id} ) ) {
956 warn "Detected loop at " . $n->id;
961 my $next = $self->next_reading( $n, $witness, $backup );
963 warn "Did not find any path for $witness from reading " . $n->id;
966 push( @readings, $next );
969 # Check that the last reading is our end reading.
970 my $last = $readings[$#readings];
971 warn "Last reading found from " . $start->text .
972 " for witness $witness is not the end!"
973 unless $last->id eq $end->id;
978 =head2 next_reading( $reading, $sigil );
980 Returns the reading that follows the given reading along the given witness
986 # Return the successor via the corresponding path.
988 my $answer = $self->_find_linked_reading( 'next', @_ );
989 return undef unless $answer;
990 return $self->reading( $answer );
993 =head2 prior_reading( $reading, $sigil )
995 Returns the reading that precedes the given reading along the given witness
1001 # Return the predecessor via the corresponding path.
1003 my $answer = $self->_find_linked_reading( 'prior', @_ );
1004 return $self->reading( $answer );
1007 sub _find_linked_reading {
1008 my( $self, $direction, $node, $path, $alt_path ) = @_;
1009 my @linked_paths = $direction eq 'next'
1010 ? $self->sequence->edges_from( $node )
1011 : $self->sequence->edges_to( $node );
1012 return undef unless scalar( @linked_paths );
1014 # We have to find the linked path that contains all of the
1015 # witnesses supplied in $path.
1016 my( @path_wits, @alt_path_wits );
1017 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1018 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1021 foreach my $le ( @linked_paths ) {
1022 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1025 my @le_wits = $self->path_witnesses( $le );
1026 if( _is_within( \@path_wits, \@le_wits ) ) {
1027 # This is the right path.
1028 return $direction eq 'next' ? $le->[1] : $le->[0];
1029 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1033 # Got this far? Return the alternate path if it exists.
1034 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1037 # Got this far? Return the base path if it exists.
1038 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1041 # Got this far? We have no appropriate path.
1042 warn "Could not find $direction node from " . $node->id
1043 . " along path $path";
1049 my( $set1, $set2 ) = @_;
1050 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1051 foreach my $el ( @$set1 ) {
1052 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1057 # Return the string that joins together a list of witnesses for
1058 # display on a single path.
1059 sub _witnesses_of_label {
1060 my( $self, $label ) = @_;
1061 my $regex = $self->wit_list_separator;
1062 my @answer = split( /\Q$regex\E/, $label );
1067 =head1 INITIALIZATION METHODS
1069 These are mostly for use by parsers.
1071 =head2 make_witness_path( $witness )
1073 Link the array of readings contained in $witness->path (and in
1074 $witness->uncorrected_path if it exists) into collation paths.
1075 Clear out the arrays when finished.
1077 =head2 make_witness_paths
1079 Call make_witness_path for all witnesses in the tradition.
1083 # For use when a collation is constructed from a base text and an apparatus.
1084 # We have the sequences of readings and just need to add path edges.
1085 # When we are done, clear out the witness path attributes, as they are no
1087 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1089 sub make_witness_paths {
1091 foreach my $wit ( $self->tradition->witnesses ) {
1092 # print STDERR "Making path for " . $wit->sigil . "\n";
1093 $self->make_witness_path( $wit );
1097 sub make_witness_path {
1098 my( $self, $wit ) = @_;
1099 my @chain = @{$wit->path};
1100 my $sig = $wit->sigil;
1101 foreach my $idx ( 0 .. $#chain-1 ) {
1102 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1104 if( $wit->is_layered ) {
1105 @chain = @{$wit->uncorrected_path};
1106 foreach my $idx( 0 .. $#chain-1 ) {
1107 my $source = $chain[$idx];
1108 my $target = $chain[$idx+1];
1109 $self->add_path( $source, $target, $sig.$self->ac_label )
1110 unless $self->has_path( $source, $target, $sig );
1114 $wit->clear_uncorrected_path;
1117 =head2 calculate_ranks
1119 Calculate the reading ranks (that is, their aligned positions relative
1120 to each other) for the graph. This can only be called on linear collations.
1124 sub calculate_ranks {
1126 # Walk a version of the graph where every node linked by a relationship
1127 # edge is fundamentally the same node, and do a topological ranking on
1128 # the nodes in this graph.
1129 my $topo_graph = Graph->new();
1133 foreach my $r ( $self->readings ) {
1134 next if exists $rel_containers{$r->id};
1135 my @rels = $r->related_readings( 'colocated' );
1137 # Make a relationship container.
1139 my $rn = 'rel_container_' . $rel_ctr++;
1140 $topo_graph->add_vertex( $rn );
1142 $rel_containers{$_->id} = $rn;
1145 # Add a new node to mirror the old node.
1146 $rel_containers{$r->id} = $r->id;
1147 $topo_graph->add_vertex( $r->id );
1152 foreach my $r ( $self->readings ) {
1153 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1154 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1155 $rel_containers{$n} );
1156 # $DB::single = 1 unless $tfrom && $tto;
1157 $topo_graph->add_edge( $tfrom, $tto );
1161 # Now do the rankings, starting with the start node.
1162 my $topo_start = $rel_containers{$self->start->id};
1163 my $node_ranks = { $topo_start => 0 };
1164 my @curr_origin = ( $topo_start );
1165 # A little iterative function.
1166 while( @curr_origin ) {
1167 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1169 # Transfer our rankings from the topological graph to the real one.
1170 foreach my $r ( $self->readings ) {
1171 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1172 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1174 die "No rank calculated for node " . $r->id
1175 . " - do you have a cycle in the graph?";
1181 my( $graph, $node_ranks, @current_nodes ) = @_;
1182 # Look at each of the children of @current_nodes. If all the child's
1183 # parents have a rank, assign it the highest rank + 1 and add it to
1184 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1185 # parent gets a rank.
1187 foreach my $c ( @current_nodes ) {
1188 warn "Current reading $c has no rank!"
1189 unless exists $node_ranks->{$c};
1190 # print STDERR "Looking at child of node $c, rank "
1191 # . $node_ranks->{$c} . "\n";
1192 foreach my $child ( $graph->successors( $c ) ) {
1193 next if exists $node_ranks->{$child};
1194 my $highest_rank = -1;
1196 foreach my $parent ( $graph->predecessors( $child ) ) {
1197 if( exists $node_ranks->{$parent} ) {
1198 $highest_rank = $node_ranks->{$parent}
1199 if $highest_rank <= $node_ranks->{$parent};
1206 my $c_rank = $highest_rank + 1;
1207 # print STDERR "Assigning rank $c_rank to node $child \n";
1208 $node_ranks->{$child} = $c_rank;
1209 push( @next_nodes, $child );
1215 =head2 flatten_ranks
1217 A convenience method for parsing collation data. Searches the graph for readings
1218 with the same text at the same rank, and merges any that are found.
1224 my %unique_rank_rdg;
1225 foreach my $rdg ( $self->readings ) {
1226 next unless $rdg->has_rank;
1227 my $key = $rdg->rank . "||" . $rdg->text;
1228 if( exists $unique_rank_rdg{$key} ) {
1230 # print STDERR "Combining readings at same rank: $key\n";
1231 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1233 $unique_rank_rdg{$key} = $rdg;
1239 =head1 UTILITY FUNCTIONS
1241 =head2 common_predecessor( $reading_a, $reading_b )
1243 Find the last reading that occurs in sequence before both the given readings.
1245 =head2 common_successor( $reading_a, $reading_b )
1247 Find the first reading that occurs in sequence after both the given readings.
1251 use Text::Tradition;
1253 my $cxfile = 't/data/Collatex-16.xml';
1254 my $t = Text::Tradition->new(
1256 'input' => 'CollateX',
1259 my $c = $t->collation;
1261 is( $c->common_predecessor( 'n9', 'n23' )->id,
1262 'n20', "Found correct common predecessor" );
1263 is( $c->common_successor( 'n9', 'n23' )->id,
1264 '#END#', "Found correct common successor" );
1266 is( $c->common_predecessor( 'n19', 'n17' )->id,
1267 'n16', "Found correct common predecessor for readings on same path" );
1268 is( $c->common_successor( 'n21', 'n26' )->id,
1269 '#END#', "Found correct common successor for readings on same path" );
1275 ## Return the closest reading that is a predecessor of both the given readings.
1276 sub common_predecessor {
1278 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1279 return $self->common_in_path( $r1, $r2, 'predecessors' );
1282 sub common_successor {
1284 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1285 return $self->common_in_path( $r1, $r2, 'successors' );
1288 sub common_in_path {
1289 my( $self, $r1, $r2, $dir ) = @_;
1290 my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
1291 $iter = $self->end->rank - $iter if $dir eq 'successors';
1293 my @last_checked = ( $r1, $r2 );
1295 while( !@candidates ) {
1297 foreach my $lc ( @last_checked ) {
1298 foreach my $p ( $lc->$dir ) {
1299 if( $all_seen{$p->id} ) {
1300 push( @candidates, $p );
1302 $all_seen{$p->id} = 1;
1303 push( @new_lc, $p );
1307 @last_checked = @new_lc;
1309 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1310 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1314 __PACKAGE__->meta->make_immutable;
1320 =item * Get rid of $backup in reading_sequence