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',
77 isa => 'Text::Tradition::Collation::Reading',
78 writer => '_set_start',
84 isa => 'Text::Tradition::Collation::Reading',
91 Text::Tradition::Collation - a software model for a text collation
96 my $t = Text::Tradition->new(
97 'name' => 'this is a text',
99 'file' => '/path/to/tei_parallel_seg_file.xml' );
101 my $c = $t->collation;
102 my @readings = $c->readings;
103 my @paths = $c->paths;
104 my @relationships = $c->relationships;
106 my $svg_variant_graph = $t->collation->as_svg();
110 Text::Tradition is a library for representation and analysis of collated
111 texts, particularly medieval ones. The Collation is the central feature of
112 a Tradition, where the text, its sequence of readings, and its relationships
113 between readings are actually kept.
119 The constructor. Takes a hash or hashref of the following arguments:
123 =item * tradition - The Text::Tradition object to which the collation
126 =item * linear - Whether the collation should be linear; that is, whether
127 transposed readings should be treated as two linked readings rather than one,
128 and therefore whether the collation graph is acyclic. Defaults to true.
130 =item * baselabel - The default label for the path taken by a base text
131 (if any). Defaults to 'base text'.
133 =item * wit_list_separator - The string to join a list of witnesses for
134 purposes of making labels in display graphs. Defaults to ', '.
136 =item * ac_label - The extra label to tack onto a witness sigil when
137 representing another layer of path for the given witness - that is, when
138 a text has more than one possible reading due to scribal corrections or
139 the like. Defaults to ' (a.c.)'.
149 =head2 wit_list_separator
155 Simple accessors for collation attributes.
159 The meta-reading at the start of every witness path.
163 The meta-reading at the end of every witness path.
167 Returns all Reading objects in the graph.
169 =head2 reading( $id )
171 Returns the Reading object corresponding to the given ID.
173 =head2 add_reading( $reading_args )
175 Adds a new reading object to the collation.
176 See L<Text::Tradition::Collation::Reading> for the available arguments.
178 =head2 del_reading( $object_or_id )
180 Removes the given reading from the collation, implicitly removing its
181 paths and relationships.
183 =head2 merge_readings( $main, $second )
185 Merges the $second reading into the $main one.
186 The arguments may be either readings or reading IDs.
188 =head2 has_reading( $id )
190 Predicate to see whether a given reading ID is in the graph.
192 =head2 reading_witnesses( $object_or_id )
194 Returns a list of sigils whose witnesses contain the reading.
198 Returns all reading paths within the document - that is, all edges in the
199 collation graph. Each path is an arrayref of [ $source, $target ] reading IDs.
201 =head2 add_path( $source, $target, $sigil )
203 Links the given readings in the collation in sequence, under the given witness
204 sigil. The readings may be specified by object or ID.
206 =head2 del_path( $source, $target, $sigil )
208 Links the given readings in the collation in sequence, under the given witness
209 sigil. The readings may be specified by object or ID.
211 =head2 has_path( $source, $target );
213 Returns true if the two readings are linked in sequence in any witness.
214 The readings may be specified by object or ID.
218 Returns all Relationship objects in the collation.
220 =head2 add_relationship( $reading, $other_reading, $options )
222 Adds a new relationship of the type given in $options between the two readings,
223 which may be specified by object or ID. Returns a value of ( $status, @vectors)
224 where $status is true on success, and @vectors is a list of relationship edges
225 that were ultimately added.
226 See L<Text::Tradition::Collation::Relationship> for the available options.
232 $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
233 $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
234 $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
237 ### Reading construct/destruct functions
240 my( $self, $reading ) = @_;
241 unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
242 my %args = %$reading;
243 $reading = Text::Tradition::Collation::Reading->new(
244 'collation' => $self,
247 # First check to see if a reading with this ID exists.
248 if( $self->reading( $reading->id ) ) {
249 warn "Collation already has a reading with id " . $reading->id;
252 $self->_add_reading( $reading->id => $reading );
253 # Once the reading has been added, put it in both graphs.
254 $self->sequence->add_vertex( $reading->id );
255 $self->relations->add_reading( $reading->id );
259 around del_reading => sub {
264 if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
267 # Remove the reading from the graphs.
268 $self->sequence->delete_vertex( $arg );
269 $self->relations->delete_reading( $arg );
272 $self->$orig( $arg );
275 # merge_readings( $main, $to_be_deleted );
280 # We only need the IDs for adding paths to the graph, not the reading
281 # objects themselves.
282 my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
284 # The kept reading should inherit the paths and the relationships
285 # of the deleted reading.
286 foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
287 my @vector = ( $kept );
288 push( @vector, $path->[1] ) if $path->[0] eq $deleted;
289 unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
290 next if $vector[0] eq $vector[1]; # Don't add a self loop
291 my %wits = %{$self->sequence->get_edge_attributes( @$path )};
292 $self->sequence->add_edge( @vector );
293 my $fwits = $self->sequence->get_edge_attributes( @vector );
294 @wits{keys %$fwits} = values %$fwits;
295 $self->sequence->set_edge_attributes( @vector, \%wits );
297 $self->relations->merge_readings( $kept, $deleted, $combine_char );
299 # Do the deletion deed.
300 if( $combine_char ) {
301 my $kept_obj = $self->reading( $kept );
302 my $new_text = join( $combine_char, $kept_obj->text,
303 $self->reading( $deleted )->text );
304 $kept_obj->alter_text( $new_text );
306 $self->del_reading( $deleted );
310 # Helper function for manipulating the graph.
311 sub _stringify_args {
312 my( $self, $first, $second, $arg ) = @_;
314 if ref( $first ) eq 'Text::Tradition::Collation::Reading';
315 $second = $second->id
316 if ref( $second ) eq 'Text::Tradition::Collation::Reading';
317 return( $first, $second, $arg );
320 # Helper function for manipulating the graph.
321 sub _objectify_args {
322 my( $self, $first, $second, $arg ) = @_;
323 $first = $self->reading( $first )
324 unless ref( $first ) eq 'Text::Tradition::Collation::Reading';
325 $second = $self->reading( $second )
326 unless ref( $second ) eq 'Text::Tradition::Collation::Reading';
327 return( $first, $second, $arg );
334 # We only need the IDs for adding paths to the graph, not the reading
335 # objects themselves.
336 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
338 # Connect the readings
339 $self->sequence->add_edge( $source, $target );
340 # Note the witness in question
341 $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
347 if( ref( $_[0] ) eq 'ARRAY' ) {
354 # We only need the IDs for adding paths to the graph, not the reading
355 # objects themselves.
356 my( $source, $target, $wit ) = $self->_stringify_args( @args );
358 if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
359 $self->sequence->delete_edge_attribute( $source, $target, $wit );
361 unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
362 $self->sequence->delete_edge( $source, $target );
367 # Extra graph-alike utility
370 my( $source, $target, $wit ) = $self->_stringify_args( @_ );
371 return undef unless $self->sequence->has_edge( $source, $target );
372 return $self->sequence->has_edge_attribute( $source, $target, $wit );
375 =head2 clear_witness( @sigil_list )
377 Clear the given witnesses out of the collation entirely, removing references
378 to them in paths, and removing readings that belong only to them. Should only
379 be called via $tradition->del_witness.
384 my( $self, @sigils ) = @_;
386 # Clear the witness(es) out of the paths
387 foreach my $e ( $self->paths ) {
388 foreach my $sig ( @sigils ) {
389 $self->del_path( $e, $sig );
393 # Clear out the newly unused readings
394 foreach my $r ( $self->readings ) {
395 unless( $self->reading_witnesses( $r ) ) {
396 $self->del_reading( $r );
401 sub add_relationship {
403 my( $source, $target, $opts ) = $self->_stringify_args( @_ );
404 my( $ret, @vectors ) = $self->relations->add_relationship( $source,
405 $self->reading( $source ), $target, $self->reading( $target ), $opts );
406 # Force a full rank recalculation every time. Yuck.
407 $self->calculate_ranks() if $ret && $self->end->has_rank;
408 return( $ret, @vectors );
411 =head2 reading_witnesses( $reading )
413 Return a list of sigils corresponding to the witnesses in which the reading appears.
417 sub reading_witnesses {
418 my( $self, $reading ) = @_;
419 # We need only check either the incoming or the outgoing edges; I have
420 # arbitrarily chosen "incoming". Thus, special-case the start node.
421 if( $reading eq $self->start ) {
422 return map { $_->sigil } $self->tradition->witnesses;
425 foreach my $e ( $self->sequence->edges_to( $reading ) ) {
426 my $wits = $self->sequence->get_edge_attributes( @$e );
427 @all_witnesses{ keys %$wits } = 1;
429 return keys %all_witnesses;
432 =head1 OUTPUT METHODS
436 Returns an SVG string that represents the graph, via as_dot and graphviz.
443 my @cmd = qw/dot -Tsvg/;
445 my $dotfile = File::Temp->new();
447 # $dotfile->unlink_on_destroy(0);
448 binmode $dotfile, ':utf8';
449 print $dotfile $self->as_dot();
450 push( @cmd, $dotfile->filename );
451 run( \@cmd, ">", binary(), \$svg );
452 $svg = decode_utf8( $svg );
456 =head2 svg_subgraph( $from, $to )
458 Returns an SVG string that represents the portion of the graph given by the
459 specified range. The $from and $to variables refer to ranks within the graph.
464 my( $self, $from, $to ) = @_;
466 my $dot = $self->as_dot( $from, $to );
468 warn "Could not output a graph with range $from - $to";
472 my @cmd = qw/dot -Tsvg/;
474 my $dotfile = File::Temp->new();
476 # $dotfile->unlink_on_destroy(0);
477 binmode $dotfile, ':utf8';
479 push( @cmd, $dotfile->filename );
480 run( \@cmd, ">", binary(), \$svg );
481 $svg = decode_utf8( $svg );
486 =head2 as_dot( $from, $to )
488 Returns a string that is the collation graph expressed in dot
489 (i.e. GraphViz) format. If $from or $to is passed, as_dot creates
490 a subgraph rather than the entire graph.
495 my( $self, $startrank, $endrank ) = @_;
497 # Check the arguments
499 return if $endrank && $startrank > $endrank;
500 return if $startrank > $self->end->rank;
502 if( defined $endrank ) {
503 return if $endrank < 0;
504 $endrank = undef if $endrank == $self->end->rank;
507 # TODO consider making some of these things configurable
508 my $graph_name = $self->tradition->name;
509 $graph_name =~ s/[^\w\s]//g;
510 $graph_name = join( '_', split( /\s+/, $graph_name ) );
518 'fillcolor' => 'white',
523 'arrowhead' => 'open',
524 'color' => '#000000',
525 'fontcolor' => '#000000',
528 my $dot = sprintf( "digraph %s {\n", $graph_name );
529 $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
530 $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
532 # Output substitute start/end readings if necessary
534 $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
537 $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
539 my %used; # Keep track of the readings that actually appear in the graph
540 foreach my $reading ( $self->readings ) {
541 # Only output readings within our rank range.
542 next if $startrank && $reading->rank < $startrank;
543 next if $endrank && $reading->rank > $endrank;
544 $used{$reading->id} = 1;
545 # Need not output nodes without separate labels
546 next if $reading->id eq $reading->text;
547 my $label = $reading->text;
548 $label =~ s/\"/\\\"/g;
549 $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
553 my @edges = $self->paths;
554 my( %substart, %subend );
555 foreach my $edge ( @edges ) {
556 # Do we need to output this edge?
557 if( $used{$edge->[0]} && $used{$edge->[1]} ) {;
558 my $label = $self->path_display_label( $self->path_witnesses( $edge ) );
559 my $variables = { %edge_attrs, 'label' => $label };
560 # Account for the rank gap if necessary
561 if( $self->reading( $edge->[1] )->has_rank
562 && $self->reading( $edge->[0] )->has_rank
563 && $self->reading( $edge->[1] )->rank
564 - $self->reading( $edge->[0] )->rank > 1 ) {
565 $variables->{'minlen'} = $self->reading( $edge->[1] )->rank
566 - $self->reading( $edge->[0] )->rank;
568 my $varopts = _dot_attr_string( $variables );
569 $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
570 $edge->[0], $edge->[1], $varopts );
571 } elsif( $used{$edge->[0]} ) {
572 $subend{$edge->[0]} = 1;
573 } elsif( $used{$edge->[1]} ) {
574 $substart{$edge->[1]} = 1;
577 # Add substitute start and end edges if necessary
578 foreach my $node ( keys %substart ) {
579 my $witstr = $self->path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
580 my $variables = { %edge_attrs, 'label' => $witstr };
581 my $varopts = _dot_attr_string( $variables );
582 $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
584 foreach my $node ( keys %subend ) {
585 my $witstr = $self->path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
586 my $variables = { %edge_attrs, 'label' => $witstr };
587 my $varopts = _dot_attr_string( $variables );
588 $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
595 sub _dot_attr_string {
598 foreach my $k ( sort keys %$hash ) {
600 push( @attrs, $k.'="'.$v.'"' );
602 return( '[ ' . join( ', ', @attrs ) . ' ]' );
606 my( $self, @edge ) = @_;
607 # If edge is an arrayref, cope.
608 if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
612 my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
616 sub path_display_label {
617 my( $self, @wits ) = @_;
618 my $maj = scalar( $self->tradition->witnesses ) * 0.6;
619 if( scalar @wits > $maj ) {
620 # TODO break out a.c. wits
623 return join( ', ', @wits );
630 Returns a GraphML representation of the collation. The GraphML will contain
631 two graphs. The first expresses the attributes of the readings and the witness
632 paths that link them; the second expresses the relationships that link the
633 readings. This is the native transfer format for a tradition.
642 my $datafile = 't/data/florilegium_tei_ps.xml';
643 my $tradition = Text::Tradition->new( 'input' => 'TEI',
648 ok( $tradition, "Got a tradition object" );
649 is( scalar $tradition->witnesses, 13, "Found all witnesses" );
650 ok( $tradition->collation, "Tradition has a collation" );
652 my $c = $tradition->collation;
653 is( scalar $c->readings, $READINGS, "Collation has all readings" );
654 is( scalar $c->paths, $PATHS, "Collation has all paths" );
655 is( scalar $c->relationships, 0, "Collation has all relationships" );
657 # Add a few relationships
658 $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } );
659 $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } );
660 $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } );
662 # Now write it to GraphML and parse it again.
664 my $graphml = $c->as_graphml;
665 my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml );
666 is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" );
667 is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
668 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
678 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
679 my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
680 my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
681 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
683 # Create the document and root node
684 my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
685 my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
686 $graphml->setDocumentElement( $root );
687 $root->setNamespace( $xsi_ns, 'xsi', 0 );
688 $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
690 # Add the data keys for the graph
693 my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
694 foreach my $datum ( @graph_attributes ) {
695 $graph_data_keys{$datum} = 'dg'.$gdi++;
696 my $key = $root->addNewChild( $graphml_ns, 'key' );
697 $key->setAttribute( 'attr.name', $datum );
698 $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
699 $key->setAttribute( 'for', 'graph' );
700 $key->setAttribute( 'id', $graph_data_keys{$datum} );
703 # Add the data keys for nodes
710 is_start => 'boolean',
712 is_lacuna => 'boolean',
714 foreach my $datum ( keys %node_data ) {
715 $node_data_keys{$datum} = 'dn'.$ndi++;
716 my $key = $root->addNewChild( $graphml_ns, 'key' );
717 $key->setAttribute( 'attr.name', $datum );
718 $key->setAttribute( 'attr.type', $node_data{$datum} );
719 $key->setAttribute( 'for', 'node' );
720 $key->setAttribute( 'id', $node_data_keys{$datum} );
723 # Add the data keys for edges, i.e. witnesses
727 class => 'string', # Class, deprecated soon
728 witness => 'string', # ID/label for a path
729 relationship => 'string', # ID/label for a relationship
730 extra => 'boolean', # Path key
731 scope => 'string', # Relationship key
732 non_correctable => 'boolean', # Relationship key
733 non_independent => 'boolean', # Relationship key
735 foreach my $datum ( keys %edge_data ) {
736 $edge_data_keys{$datum} = 'de'.$edi++;
737 my $key = $root->addNewChild( $graphml_ns, 'key' );
738 $key->setAttribute( 'attr.name', $datum );
739 $key->setAttribute( 'attr.type', $edge_data{$datum} );
740 $key->setAttribute( 'for', 'edge' );
741 $key->setAttribute( 'id', $edge_data_keys{$datum} );
744 # Add the collation graph itself
745 my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
746 $sgraph->setAttribute( 'edgedefault', 'directed' );
747 $sgraph->setAttribute( 'id', $self->tradition->name );
748 $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
749 $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
750 $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
751 $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
752 $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
754 # Collation attribute data
755 foreach my $datum ( @graph_attributes ) {
756 my $value = $datum eq 'version' ? '3.0' : $self->$datum;
757 _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
762 # Add our readings to the graph
763 foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
764 # Add to the main graph
765 my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
766 my $node_xmlid = 'n' . $node_ctr++;
767 $node_hash{ $n->id } = $node_xmlid;
768 $node_el->setAttribute( 'id', $node_xmlid );
769 foreach my $d ( keys %node_data ) {
771 _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
776 # Add the path edges to the sequence graph
778 foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
779 # We add an edge in the graphml for every witness in $e.
780 foreach my $wit ( $self->path_witnesses( $e ) ) {
781 my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
782 $node_hash{ $e->[0] },
783 $node_hash{ $e->[1] } );
784 my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
785 $edge_el->setAttribute( 'source', $from );
786 $edge_el->setAttribute( 'target', $to );
787 $edge_el->setAttribute( 'id', $id );
789 # It's a witness path, so add the witness
791 my $key = $edge_data_keys{'witness'};
792 # Is this an ante-corr witness?
793 my $aclabel = $self->ac_label;
794 if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
795 # Keep the base witness
797 # ...and record that this is an 'extra' reading path
798 _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
800 _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
801 _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
805 # Add the relationship graph to the XML
806 $self->relations->as_graphml( $graphml_ns, $root, \%node_hash,
807 $node_data_keys{'id'}, \%edge_data_keys );
809 # Save and return the thing
810 my $result = decode_utf8( $graphml->toString(1) );
814 sub _add_graphml_data {
815 my( $el, $key, $value ) = @_;
816 return unless defined $value;
817 my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
818 $data_el->setAttribute( 'key', $key );
819 $data_el->appendText( $value );
824 Returns a CSV alignment table representation of the collation graph, one
825 row per witness (or witness uncorrected.)
831 my $table = $self->make_alignment_table;
832 my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
834 # Make the header row
835 $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
836 push( @result, decode_utf8( $csv->string ) );
837 # Make the rest of the rows
838 foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
839 my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
840 my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
841 $csv->combine( @row );
842 push( @result, decode_utf8( $csv->string ) );
844 return join( "\n", @result );
847 =head2 make_alignment_table( $use_refs, $include_witnesses )
849 Return a reference to an alignment table, in a slightly enhanced CollateX
850 format which looks like this:
852 $table = { alignment => [ { witness => "SIGIL",
853 tokens => [ { t => "TEXT" }, ... ] },
855 tokens => [ { t => "TEXT" }, ... ] },
859 If $use_refs is set to 1, the reading object is returned in the table
860 instead of READINGTEXT; if not, the text of the reading is returned.
862 If $include_witnesses is set to a hashref, only the witnesses whose sigil
863 keys have a true hash value will be included.
867 sub make_alignment_table {
868 my( $self, $noderefs, $include ) = @_;
869 unless( $self->linear ) {
870 warn "Need a linear graph in order to make an alignment table";
873 my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
874 my @all_pos = ( 1 .. $self->end->rank - 1 );
875 foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
877 next unless $include->{$wit->sigil};
879 # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
880 my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
881 my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
882 push( @{$table->{'alignment'}},
883 { 'witness' => $wit->sigil, 'tokens' => \@row } );
884 if( $wit->is_layered ) {
885 my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
886 $wit->sigil.$self->ac_label, $wit->sigil );
887 my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
888 push( @{$table->{'alignment'}},
889 { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
895 sub _make_witness_row {
896 my( $path, $positions, $noderefs ) = @_;
898 map { $char_hash{$_} = undef } @$positions;
900 foreach my $rdg ( @$path ) {
901 my $rtext = $rdg->text;
902 $rtext = '#LACUNA#' if $rdg->is_lacuna;
903 print STDERR "rank " . $rdg->rank . "\n" if $debug;
904 # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
905 $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
908 my @row = map { $char_hash{$_} } @$positions;
909 # Fill in lacuna markers for undef spots in the row
910 my $last_el = shift @row;
911 my @filled_row = ( $last_el );
912 foreach my $el ( @row ) {
913 # If we are using node reference, make the lacuna node appear many times
914 # in the table. If not, use the lacuna tag.
915 if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
916 $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
918 push( @filled_row, $el );
924 # Tiny utility function to say if a table element is a lacuna
927 return 1 if $el->{'t'} eq '#LACUNA#';
928 return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
929 && $el->{'t'}->is_lacuna;
933 # Helper to turn the witnesses along columns rather than rows. Assumes
938 return $result unless scalar @$table;
939 my $nrows = scalar @{$table->[0]};
940 foreach my $idx ( 0 .. $nrows - 1 ) {
941 foreach my $wit ( 0 .. $#{$table} ) {
942 $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
948 =head1 NAVIGATION METHODS
950 =head2 reading_sequence( $first, $last, $sigil, $backup )
952 Returns the ordered list of readings, starting with $first and ending
953 with $last, for the witness given in $sigil. If a $backup sigil is
954 specified (e.g. when walking a layered witness), it will be used wherever
955 no $sigil path exists. If there is a base text reading, that will be
956 used wherever no path exists for $sigil or $backup.
960 # TODO Think about returning some lazy-eval iterator.
961 # TODO Get rid of backup; we should know from what witness is whether we need it.
963 sub reading_sequence {
964 my( $self, $start, $end, $witness, $backup ) = @_;
966 $witness = $self->baselabel unless $witness;
967 my @readings = ( $start );
970 while( $n && $n->id ne $end->id ) {
971 if( exists( $seen{$n->id} ) ) {
972 warn "Detected loop at " . $n->id;
977 my $next = $self->next_reading( $n, $witness, $backup );
979 warn "Did not find any path for $witness from reading " . $n->id;
982 push( @readings, $next );
985 # Check that the last reading is our end reading.
986 my $last = $readings[$#readings];
987 warn "Last reading found from " . $start->text .
988 " for witness $witness is not the end!"
989 unless $last->id eq $end->id;
994 =head2 next_reading( $reading, $sigil );
996 Returns the reading that follows the given reading along the given witness
1002 # Return the successor via the corresponding path.
1004 my $answer = $self->_find_linked_reading( 'next', @_ );
1005 return undef unless $answer;
1006 return $self->reading( $answer );
1009 =head2 prior_reading( $reading, $sigil )
1011 Returns the reading that precedes the given reading along the given witness
1017 # Return the predecessor via the corresponding path.
1019 my $answer = $self->_find_linked_reading( 'prior', @_ );
1020 return $self->reading( $answer );
1023 sub _find_linked_reading {
1024 my( $self, $direction, $node, $path, $alt_path ) = @_;
1025 my @linked_paths = $direction eq 'next'
1026 ? $self->sequence->edges_from( $node )
1027 : $self->sequence->edges_to( $node );
1028 return undef unless scalar( @linked_paths );
1030 # We have to find the linked path that contains all of the
1031 # witnesses supplied in $path.
1032 my( @path_wits, @alt_path_wits );
1033 @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
1034 @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
1037 foreach my $le ( @linked_paths ) {
1038 if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
1041 my @le_wits = $self->path_witnesses( $le );
1042 if( _is_within( \@path_wits, \@le_wits ) ) {
1043 # This is the right path.
1044 return $direction eq 'next' ? $le->[1] : $le->[0];
1045 } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
1049 # Got this far? Return the alternate path if it exists.
1050 return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
1053 # Got this far? Return the base path if it exists.
1054 return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
1057 # Got this far? We have no appropriate path.
1058 warn "Could not find $direction node from " . $node->id
1059 . " along path $path";
1065 my( $set1, $set2 ) = @_;
1066 my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
1067 foreach my $el ( @$set1 ) {
1068 $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
1073 # Return the string that joins together a list of witnesses for
1074 # display on a single path.
1075 sub _witnesses_of_label {
1076 my( $self, $label ) = @_;
1077 my $regex = $self->wit_list_separator;
1078 my @answer = split( /\Q$regex\E/, $label );
1082 =head2 path_text( $sigil, $mainsigil [, $start, $end ] )
1084 Returns the text of a witness (plus its backup, if we are using a layer)
1085 as stored in the collation. The text is returned as a string, where the
1086 individual readings are joined with spaces and the meta-readings (e.g.
1087 lacunae) are omitted. Optional specification of $start and $end allows
1088 the generation of a subset of the witness text.
1093 my( $self, $wit, $backup, $start, $end ) = @_;
1094 $start = $self->start unless $start;
1095 $end = $self->end unless $end;
1096 my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit, $backup );
1097 return join( ' ', map { $_->text } @path );
1100 =head1 INITIALIZATION METHODS
1102 These are mostly for use by parsers.
1104 =head2 make_witness_path( $witness )
1106 Link the array of readings contained in $witness->path (and in
1107 $witness->uncorrected_path if it exists) into collation paths.
1108 Clear out the arrays when finished.
1110 =head2 make_witness_paths
1112 Call make_witness_path for all witnesses in the tradition.
1116 # For use when a collation is constructed from a base text and an apparatus.
1117 # We have the sequences of readings and just need to add path edges.
1118 # When we are done, clear out the witness path attributes, as they are no
1120 # TODO Find a way to replace the witness path attributes with encapsulated functions?
1122 sub make_witness_paths {
1124 foreach my $wit ( $self->tradition->witnesses ) {
1125 # print STDERR "Making path for " . $wit->sigil . "\n";
1126 $self->make_witness_path( $wit );
1130 sub make_witness_path {
1131 my( $self, $wit ) = @_;
1132 my @chain = @{$wit->path};
1133 my $sig = $wit->sigil;
1134 foreach my $idx ( 0 .. $#chain-1 ) {
1135 $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
1137 if( $wit->is_layered ) {
1138 @chain = @{$wit->uncorrected_path};
1139 foreach my $idx( 0 .. $#chain-1 ) {
1140 my $source = $chain[$idx];
1141 my $target = $chain[$idx+1];
1142 $self->add_path( $source, $target, $sig.$self->ac_label )
1143 unless $self->has_path( $source, $target, $sig );
1147 $wit->clear_uncorrected_path;
1150 =head2 calculate_ranks
1152 Calculate the reading ranks (that is, their aligned positions relative
1153 to each other) for the graph. This can only be called on linear collations.
1157 sub calculate_ranks {
1159 # Walk a version of the graph where every node linked by a relationship
1160 # edge is fundamentally the same node, and do a topological ranking on
1161 # the nodes in this graph.
1162 my $topo_graph = Graph->new();
1166 foreach my $r ( $self->readings ) {
1167 next if exists $rel_containers{$r->id};
1168 my @rels = $r->related_readings( 'colocated' );
1170 # Make a relationship container.
1172 my $rn = 'rel_container_' . $rel_ctr++;
1173 $topo_graph->add_vertex( $rn );
1175 $rel_containers{$_->id} = $rn;
1178 # Add a new node to mirror the old node.
1179 $rel_containers{$r->id} = $r->id;
1180 $topo_graph->add_vertex( $r->id );
1185 foreach my $r ( $self->readings ) {
1186 foreach my $n ( $self->sequence->successors( $r->id ) ) {
1187 my( $tfrom, $tto ) = ( $rel_containers{$r->id},
1188 $rel_containers{$n} );
1189 # $DB::single = 1 unless $tfrom && $tto;
1190 $topo_graph->add_edge( $tfrom, $tto );
1194 # Now do the rankings, starting with the start node.
1195 my $topo_start = $rel_containers{$self->start->id};
1196 my $node_ranks = { $topo_start => 0 };
1197 my @curr_origin = ( $topo_start );
1198 # A little iterative function.
1199 while( @curr_origin ) {
1200 @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
1202 # Transfer our rankings from the topological graph to the real one.
1203 foreach my $r ( $self->readings ) {
1204 if( defined $node_ranks->{$rel_containers{$r->id}} ) {
1205 $r->rank( $node_ranks->{$rel_containers{$r->id}} );
1207 die "No rank calculated for node " . $r->id
1208 . " - do you have a cycle in the graph?";
1214 my( $graph, $node_ranks, @current_nodes ) = @_;
1215 # Look at each of the children of @current_nodes. If all the child's
1216 # parents have a rank, assign it the highest rank + 1 and add it to
1217 # @next_nodes. Otherwise skip it; we will return when the highest-ranked
1218 # parent gets a rank.
1220 foreach my $c ( @current_nodes ) {
1221 warn "Current reading $c has no rank!"
1222 unless exists $node_ranks->{$c};
1223 # print STDERR "Looking at child of node $c, rank "
1224 # . $node_ranks->{$c} . "\n";
1225 foreach my $child ( $graph->successors( $c ) ) {
1226 next if exists $node_ranks->{$child};
1227 my $highest_rank = -1;
1229 foreach my $parent ( $graph->predecessors( $child ) ) {
1230 if( exists $node_ranks->{$parent} ) {
1231 $highest_rank = $node_ranks->{$parent}
1232 if $highest_rank <= $node_ranks->{$parent};
1239 my $c_rank = $highest_rank + 1;
1240 # print STDERR "Assigning rank $c_rank to node $child \n";
1241 $node_ranks->{$child} = $c_rank;
1242 push( @next_nodes, $child );
1248 =head2 flatten_ranks
1250 A convenience method for parsing collation data. Searches the graph for readings
1251 with the same text at the same rank, and merges any that are found.
1257 my %unique_rank_rdg;
1258 foreach my $rdg ( $self->readings ) {
1259 next unless $rdg->has_rank;
1260 my $key = $rdg->rank . "||" . $rdg->text;
1261 if( exists $unique_rank_rdg{$key} ) {
1263 # print STDERR "Combining readings at same rank: $key\n";
1264 $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
1266 $unique_rank_rdg{$key} = $rdg;
1272 =head1 UTILITY FUNCTIONS
1274 =head2 common_predecessor( $reading_a, $reading_b )
1276 Find the last reading that occurs in sequence before both the given readings.
1278 =head2 common_successor( $reading_a, $reading_b )
1280 Find the first reading that occurs in sequence after both the given readings.
1284 use Text::Tradition;
1286 my $cxfile = 't/data/Collatex-16.xml';
1287 my $t = Text::Tradition->new(
1289 'input' => 'CollateX',
1292 my $c = $t->collation;
1294 is( $c->common_predecessor( 'n9', 'n23' )->id,
1295 'n20', "Found correct common predecessor" );
1296 is( $c->common_successor( 'n9', 'n23' )->id,
1297 '#END#', "Found correct common successor" );
1299 is( $c->common_predecessor( 'n19', 'n17' )->id,
1300 'n16', "Found correct common predecessor for readings on same path" );
1301 is( $c->common_successor( 'n21', 'n26' )->id,
1302 '#END#', "Found correct common successor for readings on same path" );
1308 ## Return the closest reading that is a predecessor of both the given readings.
1309 sub common_predecessor {
1311 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1312 return $self->common_in_path( $r1, $r2, 'predecessors' );
1315 sub common_successor {
1317 my( $r1, $r2 ) = $self->_objectify_args( @_ );
1318 return $self->common_in_path( $r1, $r2, 'successors' );
1321 sub common_in_path {
1322 my( $self, $r1, $r2, $dir ) = @_;
1323 my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
1324 $iter = $self->end->rank - $iter if $dir eq 'successors';
1326 my @last_checked = ( $r1, $r2 );
1328 while( !@candidates ) {
1330 foreach my $lc ( @last_checked ) {
1331 foreach my $p ( $lc->$dir ) {
1332 if( $all_seen{$p->id} ) {
1333 push( @candidates, $p );
1335 $all_seen{$p->id} = 1;
1336 push( @new_lc, $p );
1340 @last_checked = @new_lc;
1342 my @answer = sort { $a->rank <=> $b->rank } @candidates;
1343 return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
1347 __PACKAGE__->meta->make_immutable;
1353 =item * Get rid of $backup in reading_sequence