X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FCollation.pm;h=3d43a846367166512e7018552b25849e638ce60a;hb=45456358649b557f9addf7193f8359f20ede6d07;hp=4bb96ca6afbd282c2236ff16de0d0c9d8978440f;hpb=dd3b58b01da8319a3e3cc31e8f99a25be101cf05;p=scpubgit%2Fstemmatology.git

diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm
index 4bb96ca..3d43a84 100644
--- a/lib/Text/Tradition/Collation.pm
+++ b/lib/Text/Tradition/Collation.pm
@@ -1,30 +1,89 @@
-#!/usr/bin/env perl
-
 package Text::Tradition::Collation;
+
+use Graph::Easy;
+use IPC::Run qw( run binary );
+use Text::Tradition::Collation::Path;
+use Text::Tradition::Collation::Reading;
+use Text::Tradition::Collation::Relationship;
+use Text::Tradition::Collation::Segment;
+use XML::LibXML;
 use Moose;
 
 has 'graph' => (
-		is => 'ro',
-		isa => 'Text::Tradition::Graph',
-		);
-
-# The graph is full of nodes, which have positions and equivalences.
-# These have to be stored externally to the graph itself.
-has 'positions' => (
-		    is => 'ro';
-		    isa => 'Text::Tradition::Graph::Position',
-		    );
-
-has 'equivalences' => (
-		       is => 'rw';
-		       isa => 'Text::Tradition::Graph::Equivalence',
-		       );
-
-# We need a way to access the parent object.
+    is => 'ro',
+    isa => 'Graph::Easy',
+    handles => {
+	add_reading => 'add_node',
+	del_reading => 'del_node',
+	add_path => 'add_edge',
+	del_path => 'del_edge',
+	reading => 'node',
+	path => 'edge',
+	readings => 'nodes',
+	segments => 'nodes',
+	paths => 'edges',
+	relationships => 'edges',
+    },
+    default => sub { Graph::Easy->new( undirected => 0 ) },
+    );
+		
+
 has 'tradition' => (
-		    is => 'ro',
-		    isa => 'Text::Tradition',
-		    );
+    is => 'rw',
+    isa => 'Text::Tradition',
+    );
+
+has 'svg' => (
+    is => 'ro',
+    isa => 'Str',
+    writer => '_save_svg',
+    predicate => 'has_svg',
+    );
+
+has 'graphml' => (
+    is => 'ro',
+    isa => 'Str',
+    writer => '_save_graphml',
+    predicate => 'has_graphml',
+    );
+
+# Keeps track of the lemmas within the collation.  At most one lemma
+# per position in the graph.
+has 'lemmata' => (
+    is => 'ro',
+    isa => 'HashRef[Maybe[Str]]',
+    default => sub { {} },
+    );
+
+has 'wit_list_separator' => (
+    is => 'rw',
+    isa => 'Str',
+    default => ', ',
+    );
+
+has 'baselabel' => (
+    is => 'rw',
+    isa => 'Str',
+    default => 'base text',
+    );
+
+has 'collapsed' => (
+    is => 'rw',
+    isa => 'Bool',
+    );
+
+has 'linear' => (
+    is => 'rw',
+    isa => 'Bool',
+    default => 1,
+    );
+
+has 'ac_label' => (
+    is => 'rw',
+    isa => 'Str',
+    default => ' (a.c.)',
+    );
+
 
 # The collation can be created two ways:
 # 1. Collate a set of witnesses (with CollateX I guess) and process
@@ -41,5 +100,944 @@ has 'tradition' => (
 # constructor will also need to make the witness objects, if we didn't
 # come through option 1.
 
+sub BUILD {
+    my( $self, $args ) = @_;
+    $self->graph->use_class('node', 'Text::Tradition::Collation::Reading');
+    $self->graph->use_class('edge', 'Text::Tradition::Collation::Path');
+
+    # Pass through any graph-specific options.
+    my $shape = exists( $args->{'shape'} ) ? $args->{'shape'} : 'ellipse';
+    $self->graph->set_attribute( 'node', 'shape', $shape );
+}
+
+# Wrapper around add_path 
+
+around add_path => sub {
+    my $orig = shift;
+    my $self = shift;
+
+    # Make sure there are three arguments
+    unless( @_ == 3 ) {
+	warn "Call add_path with args source, target, witness";
+	return;
+    }
+    # Make sure the proposed path does not yet exist
+    # NOTE 'reading' will currently return readings and segments
+    my( $source, $target, $wit ) = @_;
+    $source = $self->reading( $source )
+	unless ref( $source ) eq 'Text::Tradition::Collation::Reading';
+    $target = $self->reading( $target )
+	unless ref( $target ) eq 'Text::Tradition::Collation::Reading';
+    foreach my $path ( $source->edges_to( $target ) ) {
+	if( $path->label eq $wit && $path->class eq 'edge.path' ) {
+	    return;
+	}
+    }
+    # Do the deed
+    $self->$orig( @_ );
+};
+
+# Wrapper around paths
+around paths => sub {
+    my $orig = shift;
+    my $self = shift;
+
+    my @result = grep { $_->sub_class eq 'path' } $self->$orig( @_ );
+    return @result;
+};
+
+around relationships => sub {
+    my $orig = shift;
+    my $self = shift;
+    my @result = grep { $_->sub_class eq 'relationship' } $self->$orig( @_ );
+    return @result;
+};
+
+around readings => sub {
+    my $orig = shift;
+    my $self = shift;
+    my @result = grep { $_->sub_class ne 'segment' } $self->$orig( @_ );
+    return @result;
+};
+
+around segments => sub {
+    my $orig = shift;
+    my $self = shift;
+    my @result = grep { $_->sub_class eq 'segment' } $self->$orig( @_ );
+    return @result;
+};
+
+# Wrapper around merge_nodes
+
+sub merge_readings {
+    my $self = shift;
+    my $first_node = shift;
+    my $second_node = shift;
+    $first_node->merge_from( $second_node );
+    unshift( @_, $first_node, $second_node );
+    return $self->graph->merge_nodes( @_ );
+}
+
+# Extra graph-alike utility
+sub has_path {
+    my( $self, $source, $target, $label ) = @_;
+    my @paths = $source->edges_to( $target );
+    my @relevant = grep { $_->label eq $label } @paths;
+    return scalar @relevant;
+}
+
+## Dealing with groups of readings, i.e. segments.
+
+sub add_segment {
+    my( $self, @items ) = @_;
+    my $segment = Text::Tradition::Collation::Segment->new( 'members' => \@items );
+    return $segment;
+}
+
+## Dealing with relationships between readings.  This is a different
+## sort of graph edge.
+
+sub add_relationship {
+    my( $self, $source, $target, $options ) = @_;
+
+    # Make sure there is not another relationship between these two
+    # readings or segments already
+    $source = $self->reading( $source )
+	unless ref( $source ) && $source->isa( 'Graph::Easy::Node' );
+    $target = $self->reading( $target )
+	unless ref( $target ) && $target->isa( 'Graph::Easy::Node' );
+    foreach my $rel ( $source->edges_to( $target ) ) {
+	if( $rel->label eq $options->{'type'} && $rel->class eq 'edge.relationship' ) {
+	    return;
+	}
+    }
+    $options->{'orig_relation'} = [ $source, $target ];
+
+    my $rel = Text::Tradition::Collation::Relationship->new( %$options );
+    $self->graph->add_edge( $source, $target, $rel );
+    if( $options->{'global'} ) {
+	# Look for all readings with the source label, and if there are
+	# colocated readings with the target label, join them too.
+	foreach my $r ( $self->readings() ) {
+	    next unless $r->label eq $source->label;
+	    my @colocated = grep { $_->label eq $target->label }
+	        $self->same_position_as( $r );
+	    if( @colocated ) {
+		warn "Multiple readings with same label at same position!"
+		    if @colocated > 1;
+		my $dup_rel = Text::Tradition::Collation::Relationship->new( %$options );
+		$self->graph->add_edge( $r, $colocated[0], $dup_rel );
+	    }
+	}
+    }
+}
+
+=head2 Output method(s)
+
+=over
+
+=item B<as_svg>
+
+print $graph->as_svg( $recalculate );
+
+Returns an SVG string that represents the graph.  Uses GraphViz to do
+this, because Graph::Easy doesn\'t cope well with long graphs. Unless
+$recalculate is passed (and is a true value), the method will return a
+cached copy of the SVG after the first call to the method.
+
+=cut
+
+sub as_svg {
+    my( $self, $recalc ) = @_;
+    return $self->svg if $self->has_svg;
+    
+    $self->collapse_graph_paths();
+    
+    my @cmd = qw/dot -Tsvg/;
+    my( $svg, $err );
+    my $in = $self->as_dot();
+    run( \@cmd, \$in, ">", binary(), \$svg );
+    $self->_save_svg( $svg );
+    $self->expand_graph_paths();
+    return $svg;
+}
+
+=item B<as_dot>
+
+print $graph->as_dot( $view, $recalculate );
+
+Returns a string that is the collation graph expressed in dot
+(i.e. GraphViz) format.  The 'view' argument determines what kind of
+graph is produced.
+    * 'path': a graph of witness paths through the collation (DEFAULT)
+    * 'relationship': a graph of how collation readings relate to 
+      each other
+
+=cut
+
+sub as_dot {
+    my( $self, $view ) = @_;
+    $view = 'path' unless $view;
+    # TODO consider making some of these things configurable
+    my $dot = sprintf( "digraph %s {\n", $self->tradition->name );
+    $dot .= "\tedge [ arrowhead=open ];\n";
+    $dot .= "\tgraph [ rankdir=LR ];\n";
+    $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
+		     11, "white", "filled", $self->graph->get_attribute( 'node', 'shape' ) );
+
+    foreach my $reading ( $self->readings ) {
+	# Need not output nodes without separate labels
+	next if $reading->name eq $reading->label;
+	# TODO output readings or segments, but not both
+	next if $reading->class eq 'node.segment';
+	$dot .= sprintf( "\t\"%s\" [ label=\"%s\" ]\n", $reading->name, $reading->label );
+    }
+
+    my @edges = $view eq 'relationship' ? $self->relationships : $self->paths;
+    foreach my $edge ( @edges ) {
+	$dot .= sprintf( "\t\"%s\" -> \"%s\" [ color=\"%s\", fontcolor=\"%s\", label=\"%s\" ]\n",
+			 $edge->from->name, $edge->to->name, '#000000', '#000000', $edge->label );
+    }
+
+    $dot .= "}\n";
+    return $dot;
+}
+
+=item B<as_graphml>
+
+print $graph->as_graphml( $recalculate )
+
+Returns a GraphML representation of the collation graph, with
+transposition information and position information. Unless
+$recalculate is passed (and is a true value), the method will return a
+cached copy of the SVG after the first call to the method.
+
+=cut
+
+sub as_graphml {
+    my( $self, $recalc ) = @_;
+    return $self->graphml if $self->has_graphml;
+
+    # Some namespaces
+    my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
+    my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
+    my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
+	'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
+
+    # Create the document and root node
+    my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
+    my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
+    $graphml->setDocumentElement( $root );
+    $root->setNamespace( $xsi_ns, 'xsi', 0 );
+    $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
+
+    # Add the data keys for nodes
+    my %node_data_keys;
+    my $ndi = 0;
+    foreach my $datum ( qw/ name reading identical position class / ) {
+	$node_data_keys{$datum} = 'dn'.$ndi++;
+	my $key = $root->addNewChild( $graphml_ns, 'key' );
+	$key->setAttribute( 'attr.name', $datum );
+	$key->setAttribute( 'attr.type', 'string' );
+	$key->setAttribute( 'for', 'node' );
+	$key->setAttribute( 'id', $node_data_keys{$datum} );
+    }
+
+    # Add the data keys for edges, i.e. witnesses
+    my $edi = 0;
+    my %edge_data_keys;
+    foreach my $edge_key( qw/ witness_main witness_ante_corr relationship class / ) {
+	$edge_data_keys{$edge_key} = 'de'.$edi++;
+	my $key = $root->addNewChild( $graphml_ns, 'key' );
+	$key->setAttribute( 'attr.name', $edge_key );
+	$key->setAttribute( 'attr.type', 'string' );
+	$key->setAttribute( 'for', 'edge' );
+	$key->setAttribute( 'id', $edge_data_keys{$edge_key} );
+    }
+    
+    # Add the graph, its nodes, and its edges
+    my $graph = $root->addNewChild( $graphml_ns, 'graph' );
+    $graph->setAttribute( 'edgedefault', 'directed' );
+    $graph->setAttribute( 'id', 'g0' ); # TODO make this meaningful
+    $graph->setAttribute( 'parse.edgeids', 'canonical' );
+    $graph->setAttribute( 'parse.edges', scalar($self->paths) );
+    $graph->setAttribute( 'parse.nodeids', 'canonical' );
+    $graph->setAttribute( 'parse.nodes', scalar($self->readings) );
+    $graph->setAttribute( 'parse.order', 'nodesfirst' );
+
+    my $node_ctr = 0;
+    my %node_hash;
+    # Add our readings to the graph
+    foreach my $n ( sort { $a->name cmp $b->name } $self->readings ) {
+	my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
+	my $node_xmlid = 'n' . $node_ctr++;
+	$node_hash{ $n->name } = $node_xmlid;
+	$node_el->setAttribute( 'id', $node_xmlid );
+	_add_graphml_data( $node_el, $node_data_keys{'name'}, $n->name );
+	_add_graphml_data( $node_el, $node_data_keys{'reading'}, $n->label );
+	_add_graphml_data( $node_el, $node_data_keys{'position'}, $n->position );
+	_add_graphml_data( $node_el, $node_data_keys{'class'}, $n->sub_class );
+	_add_graphml_data( $node_el, $node_data_keys{'identical'}, $n->primary->name )
+	    if $n->has_primary;
+    }
+
+    # Add any segments we have
+    foreach my $n ( sort { $a->name cmp $b->name } $self->segments ) {
+	my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
+	my $node_xmlid = 'n' . $node_ctr++;
+	$node_hash{ $n->name } = $node_xmlid;
+	$node_el->setAttribute( 'id', $node_xmlid );
+	_add_graphml_data( $node_el, $node_data_keys{'class'}, $n->sub_class );
+	_add_graphml_data( $node_el, $node_data_keys{'name'}, $n->name );
+    }
+
+    # Add the path, relationship, and segment edges
+    my $edge_ctr = 0;
+    foreach my $e ( sort { $a->from->name cmp $b->from->name } $self->graph->edges() ) {
+	my( $name, $from, $to ) = ( 'e'.$edge_ctr++,
+				    $node_hash{ $e->from->name() },
+				    $node_hash{ $e->to->name() } );
+	my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
+	$edge_el->setAttribute( 'source', $from );
+	$edge_el->setAttribute( 'target', $to );
+	$edge_el->setAttribute( 'id', $name );
+	# Add the edge class
+	_add_graphml_data( $edge_el, $edge_data_keys{'class'}, $e->sub_class );
+	if( $e->sub_class eq 'path' ) {
+	    # It's a witness path, so add the witness
+	    my $base = $e->label;
+	    my $key = $edge_data_keys{'witness_main'};
+	    # TODO kind of hacky
+	    if( $e->label =~ /^(.*?)\s+(\(a\.c\.\))$/ ) {
+		$base = $1;
+		$key = $edge_data_keys{'witness_ante_corr'};
+	    }
+	    _add_graphml_data( $edge_el, $key, $base );
+	} elsif( $e->sub_class eq 'relationship' ) {
+	    # It's a relationship
+	    _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $e->label );
+	} # else a segment, nothing to record but source, target, class
+    }
+
+    # Return the thing
+    $self->_save_graphml( $graphml->toString(1) );
+    return $graphml->toString(1);
+}
+
+sub _add_graphml_data {
+    my( $el, $key, $value ) = @_;
+    my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
+    return unless defined $value;
+    $data_el->setAttribute( 'key', $key );
+    $data_el->appendText( $value );
+}
+
+sub collapse_graph_paths {
+    my $self = shift;
+    # Our collation graph has an path per witness.  This is great for
+    # calculation purposes, but terrible for display.  Thus we want to
+    # display only one path between any two nodes.
+
+    return if $self->collapsed;
+
+    print STDERR "Collapsing witness paths in graph...\n";
+
+    # Don't list out every witness if we have more than half to list.
+    my $majority = int( scalar( @{$self->tradition->witnesses} ) / 2 ) + 1;
+    # But don't compress if there are only a few witnesses.
+    $majority = 4 if $majority < 4;
+    foreach my $node ( $self->readings ) {
+	my $newlabels = {};
+	# We will visit each node, so we only look ahead.
+	foreach my $edge ( $node->outgoing() ) {
+	    next unless $edge->class eq 'edge.path';
+	    add_hash_entry( $newlabels, $edge->to->name, $edge->name );
+	    $self->del_path( $edge );
+	}
+
+	foreach my $newdest ( keys %$newlabels ) {
+	    my $label;
+	    my @compressed_wits = ();
+	    if( @{$newlabels->{$newdest}} < $majority ) {
+		$label = join( ', ', sort( @{$newlabels->{$newdest}} ) );
+	    } else {
+		## TODO FIX THIS HACK
+		my @aclabels;
+		foreach my $wit ( @{$newlabels->{$newdest}} ) {
+		    if( $wit =~ /^(.*?)(\s*\(?a\.\s*c\.\)?)$/ ) {
+			push( @aclabels, $wit );
+		    } else {
+			push( @compressed_wits, $wit );
+		    }
+		}
+		$label = join( ', ', 'majority', sort( @aclabels ) );
+	    }
+	    
+	    my $newpath = 
+		$self->add_path( $node, $self->reading( $newdest ), $label );
+	    if( @compressed_wits ) {
+		$newpath->hidden_witnesses( \@compressed_wits );
+	    }
+	}
+    }
+
+    $self->collapsed( 1 );
+}
+
+sub expand_graph_paths {
+    my $self = shift;
+    # Our collation graph has only one path between any two nodes.
+    # This is great for display, but not so great for analysis.
+    # Expand this so that each witness has its own path between any
+    # two reading nodes.
+    return unless $self->collapsed;
+    
+    print STDERR "Expanding witness paths in graph...\n";
+    foreach my $path( $self->paths ) {
+	my $from = $path->from;
+	my $to = $path->to;
+	my @wits = split( /, /, $path->label );
+	if( $path->has_hidden_witnesses ) {
+	    push( @wits, @{$path->hidden_witnesses} );
+	}
+	$self->del_path( $path );
+	foreach ( @wits ) {
+	    $self->add_path( $from, $to, $_ );
+	}
+    }
+    $self->collapsed( 0 );
+}
+
+=back
+
+=head2 Navigation methods
+
+=over
+
+=item B<start>
+
+my $beginning = $collation->start();
+
+Returns the beginning of the collation, a meta-reading with label '#START#'.
+
+=cut
+
+sub start {
+    # Return the beginning reading of the graph.
+    my $self = shift;
+    my( $new_start ) = @_;
+    if( $new_start ) {
+	$self->del_reading( '#START#' );
+	$self->graph->rename_node( $new_start, '#START#' );
+    }
+    return $self->reading('#START#');
+}
+
+=item B<reading_sequence>
+
+my @readings = $graph->reading_sequence( $first, $last, $path[, $alt_path] );
+
+Returns the ordered list of readings, starting with $first and ending
+with $last, along the given witness path.  If no path is specified,
+assume that the path is that of the base text (if any.)
+
+=cut
+
+sub reading_sequence {
+    my( $self, $start, $end, $witness, $backup ) = @_;
+
+    $witness = $self->baselabel unless $witness;
+    my @readings = ( $start );
+    my %seen;
+    my $n = $start;
+    while( $n && $n ne $end ) {
+	if( exists( $seen{$n->name()} ) ) {
+	    warn "Detected loop at " . $n->name();
+	    last;
+	}
+	$seen{$n->name()} = 1;
+	
+	my $next = $self->next_reading( $n, $witness, $backup );
+	warn "Did not find any path for $witness from reading " . $n->name
+	    unless $next;
+	push( @readings, $next );
+	$n = $next;
+    }
+    # Check that the last reading is our end reading.
+    my $last = $readings[$#readings];
+    warn "Last reading found from " . $start->label() .
+	" for witness $witness is not the end!"
+	unless $last eq $end;
+    
+    return @readings;
+}
+
+=item B<next_reading>
+
+my $next_reading = $graph->next_reading( $reading, $witpath );
+
+Returns the reading that follows the given reading along the given witness
+path.  
+
+=cut
+
+sub next_reading {
+    # Return the successor via the corresponding path.
+    my $self = shift;
+    return $self->_find_linked_reading( 'next', @_ );
+}
+
+=item B<prior_reading>
+
+my $prior_reading = $graph->prior_reading( $reading, $witpath );
+
+Returns the reading that precedes the given reading along the given witness
+path.  
+
+=cut
+
+sub prior_reading {
+    # Return the predecessor via the corresponding path.
+    my $self = shift;
+    return $self->_find_linked_reading( 'prior', @_ );
+}
+
+sub _find_linked_reading {
+    my( $self, $direction, $node, $path, $alt_path ) = @_;
+    my @linked_paths = $direction eq 'next' 
+	? $node->outgoing() : $node->incoming();
+    return undef unless scalar( @linked_paths );
+    
+    # We have to find the linked path that contains all of the
+    # witnesses supplied in $path.
+    my( @path_wits, @alt_path_wits );
+    @path_wits = $self->witnesses_of_label( $path ) if $path;
+    @alt_path_wits = $self->witnesses_of_label( $alt_path ) if $alt_path;
+    my $base_le;
+    my $alt_le;
+    foreach my $le ( @linked_paths ) {
+	if( $le->name eq $self->baselabel ) {
+	    $base_le = $le;
+	} else {
+	    my @le_wits = $self->witnesses_of_label( $le->name );
+	    if( _is_within( \@path_wits, \@le_wits ) ) {
+		# This is the right path.
+		return $direction eq 'next' ? $le->to() : $le->from();
+	    } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
+		$alt_le = $le;
+	    }
+	}
+    }
+    # Got this far? Return the alternate path if it exists.
+    return $direction eq 'next' ? $alt_le->to() : $alt_le->from()
+	if $alt_le;
+
+    # Got this far? Return the base path if it exists.
+    return $direction eq 'next' ? $base_le->to() : $base_le->from()
+	if $base_le;
+
+    # Got this far? We have no appropriate path.
+    warn "Could not find $direction node from " . $node->label 
+	. " along path $path";
+    return undef;
+}
+
+# Some set logic.
+sub _is_within {
+    my( $set1, $set2 ) = @_;
+    my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
+    foreach my $el ( @$set1 ) {
+	$ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
+    }
+    return $ret;
+}
+
+
+## INITIALIZATION METHODS - for use by parsers
+# Walk the paths for each witness in the graph, and return the nodes
+# that the graph has in common.  If $using_base is true, some 
+# different logic is needed.
+
+sub walk_witness_paths {
+    my( $self, $end ) = @_;
+    # For each witness, walk the path through the graph.
+    # Then we need to find the common nodes.  
+    # TODO This method is going to fall down if we have a very gappy 
+    # text in the collation.
+    my $paths = {};
+    my @common_readings;
+    foreach my $wit ( @{$self->tradition->witnesses} ) {
+	my $curr_reading = $self->start;
+	my @wit_path = $self->reading_sequence( $self->start, $end, 
+						$wit->sigil );
+	$wit->path( \@wit_path );
+
+	# Detect the common readings.
+	@common_readings = _find_common( \@common_readings, \@wit_path );
+    }
+
+    # Mark all the nodes as either common or not.
+    foreach my $cn ( @common_readings ) {
+	print STDERR "Setting " . $cn->name . " / " . $cn->label 
+	    . " as common node\n";
+	$cn->make_common;
+    }
+    foreach my $n ( $self->readings() ) {
+	$n->make_variant unless $n->is_common;
+    }
+    # Return an array of the common nodes in order.
+    return @common_readings;
+}
+
+sub _find_common {
+    my( $common_readings, $new_path ) = @_;
+    my @cr;
+    if( @$common_readings ) {
+	foreach my $n ( @$new_path ) {
+	    push( @cr, $n ) if grep { $_ eq $n } @$common_readings;
+	}
+    } else {
+	push( @cr, @$new_path );
+    }
+    return @cr;
+}
+
+sub _remove_common {
+    my( $common_readings, $divergence ) = @_;
+    my @cr;
+    my %diverged;
+    map { $diverged{$_->name} = 1 } @$divergence;
+    foreach( @$common_readings ) {
+	push( @cr, $_ ) unless $diverged{$_->name};
+    }
+    return @cr;
+}
+
+
+# An alternative to walk_witness_paths, for use when a collation is
+# constructed from a base text and an apparatus.  We have the
+# sequences of readings and just need to add path edges.
+
+sub make_witness_paths {
+    my( $self ) = @_;
+
+    my @common_readings;
+    foreach my $wit ( @{$self->tradition->witnesses} ) {
+	print STDERR "Making path for " . $wit->sigil . "\n";
+	$self->make_witness_path( $wit );
+	@common_readings = _find_common( \@common_readings, $wit->path );
+	@common_readings = _find_common( \@common_readings, $wit->uncorrected_path );
+    }
+    map { $_->make_common } @common_readings;
+    return @common_readings;
+}
+
+sub make_witness_path {
+    my( $self, $wit ) = @_;
+    my @chain = @{$wit->path};
+    my $sig = $wit->sigil;
+    foreach my $idx ( 0 .. $#chain-1 ) {
+	$self->add_path( $chain[$idx], $chain[$idx+1], $sig );
+    }
+    @chain = @{$wit->uncorrected_path};
+    foreach my $idx( 0 .. $#chain-1 ) {
+	my $source = $chain[$idx];
+	my $target = $chain[$idx+1];
+	$self->add_path( $source, $target, $sig.$self->ac_label )
+	    unless $self->has_path( $source, $target, $sig );
+    }
+}
+
+sub common_readings {
+    my $self = shift;
+    my @common = grep { $_->is_common } $self->readings();
+    return sort { _cmp_position( $a->position, $b->position ) } @common;
+}
+
+# Calculate the relative positions of nodes in the graph, if they
+# were not given to us.
+sub calculate_positions {
+    my( $self, @ordered_common ) = @_;
+
+    # We have to calculate the position identifiers for each word,
+    # keyed on the common nodes.  This will be 'fun'.  The end result
+    # is a hash per witness, whose key is the word node and whose
+    # value is its position in the text.  Common nodes are always N,1
+    # so have identical positions in each text.
+
+    my $node_pos = {};
+    foreach my $wit ( @{$self->tradition->witnesses} ) {
+	print STDERR "Calculating positions in " . $wit->sigil . "\n";
+	_update_positions_from_path( $wit->path, @ordered_common );
+	_update_positions_from_path( $wit->uncorrected_path, @ordered_common )
+	    if $wit->has_ante_corr;
+    }
+    
+    # DEBUG
+    foreach my $r ( $self->readings() ) {
+	print STDERR "Reading " . $r->name . "/" . $r->label . " has no position\n"
+	    unless( $r->has_position );
+    }
+
+    $self->init_lemmata();
+}
+
+sub _update_positions_from_path {
+    my( $path, @ordered_common ) = @_;
+
+    # First we walk the given path, making a matrix for the witness
+    # that corresponds to its eventual position identifier.  Common
+    # nodes always start a new row, and are thus always in the first
+    # column.
+    my $wit_matrix = [];
+    my $cn = 0;  # We should hit the common readings in order.
+    my $row = [];
+    foreach my $wn ( @{$path} ) {
+	if( $wn eq $ordered_common[$cn] ) {
+	    # Set up to look for the next common node, and
+	    # start a new row of words.
+	    $cn++;
+	    push( @$wit_matrix, $row ) if scalar( @$row );
+	    $row = [];
+	}
+	push( @$row, $wn );
+    }
+    push( @$wit_matrix, $row );  # Push the last row onto the matrix
+
+    # Now we have a matrix per witness, so that each row in the
+    # matrix begins with a common node, and continues with all the
+    # variant words that appear in the witness.  We turn this into
+    # real positions in row,cell format.  But we need some
+    # trickery in order to make sure that each node gets assigned
+    # to only one position.
+    
+    foreach my $li ( 1..scalar(@$wit_matrix) ) {
+	foreach my $di ( 1..scalar(@{$wit_matrix->[$li-1]}) ) {
+	    my $reading = $wit_matrix->[$li-1]->[$di-1];
+	    my $position = "$li,$di";
+
+	    # If we have seen this node before, we need to compare
+	    # its position with what went before.
+	    unless( $reading->has_position &&
+		    _cmp_position( $position, $reading->position ) < 1 ) {
+		# The new position ID replaces the old one.
+		$reading->position( $position );
+	    } # otherwise, the old position needs to stay.
+	}
+    }
+}
+
+sub _cmp_position {
+    my( $a, $b ) = @_;
+    if ( $a && $b ) {
+	my @pos_a = split(/,/, $a );
+	my @pos_b = split(/,/, $b );
+
+	my $big_cmp = $pos_a[0] <=> $pos_b[0];
+	return $big_cmp if $big_cmp;
+	# else 
+	return $pos_a[1] <=> $pos_b[1];
+    } elsif ( $b ) { # a is undefined
+	return -1;
+    } elsif ( $a ) { # b is undefined
+	return 1;
+    }
+    return 0; # they are both undefined
+}
+
+sub all_positions {
+    my $self = shift;
+    my %positions = ();
+    map { $positions{$_->position} = 1 } $self->readings;
+    my @answer = sort { _cmp_position( $a, $b ) } keys( %positions );
+    return @answer;
+}
+
+sub readings_at_position {
+    my( $self, $pos ) = @_;
+    my @answer = grep { $_->position eq $pos } $self->readings;
+    return @answer;
+}
+
+## Lemmatizer functions
+
+sub init_lemmata {
+    my $self = shift;
+    
+    foreach my $position ( $self->all_positions ) {
+	$self->lemmata->{$position} = undef;
+    }
+
+    foreach my $cr ( $self->common_readings ) {
+	$self->lemmata->{$cr->position} = $cr->name;
+    }
+}
+    
+=item B<lemma_readings>
+
+my @state = $graph->lemma_readings( @readings_delemmatized );
+
+Takes a list of readings that have just been delemmatized, and returns
+a set of tuples of the form ['reading', 'state'] that indicates what
+changes need to be made to the graph.
+
+=over
+
+=item * 
+
+A state of 1 means 'lemmatize this reading'
+
+=item * 
+
+A state of 0 means 'delemmatize this reading'
+
+=item * 
+
+A state of undef means 'an ellipsis belongs in the text here because
+no decision has been made / an earlier decision was backed out'
+
+=back
+
+=cut
+
+sub lemma_readings {
+    my( $self, @toggled_off_nodes ) = @_;
+
+    # First get the positions of those nodes which have been
+    # toggled off.
+    my $positions_off = {};
+    map { $positions_off->{ $_->position } = $_->name } @toggled_off_nodes;
+
+    # Now for each position, we have to see if a node is on, and we
+    # have to see if a node has been turned off.
+    my @answer;
+    foreach my $pos ( $self->all_positions() ) {
+	# Find the state of this position.  If there is an active node,
+	# its name will be the state; otherwise the state will be 0 
+	# (nothing at this position) or undef (ellipsis at this position)
+	my $active = $self->lemmata->{$pos};
+	
+	# Is there a formerly active node that was toggled off?
+	if( exists( $positions_off->{$pos} ) ) {
+	    my $off_node = $positions_off->{$pos};
+	    if( $active && $active ne $off_node) {
+		push( @answer, [ $off_node, 0 ], [ $active, 1 ] );
+	    } else {
+		push( @answer, [ $off_node, $active ] );
+	    }
+
+	# No formerly active node, so we just see if there is a currently
+	# active one.
+	} elsif( $active ) {
+	    # Push the active node, whatever it is.
+	    push( @answer, [ $active, 1 ] );
+	} else {
+	    # Push the state that is there. Arbitrarily use the first node
+	    # at that position.
+	    my @pos_nodes = $self->readings_at_position( $pos );
+	    push( @answer, [ $pos_nodes[0]->name, $self->lemmata->{$pos} ] );
+	}
+    }
+    
+    return @answer;
+}
+
+=item B<toggle_reading>
+
+my @readings_delemmatized = $graph->toggle_reading( $reading_name );
+
+Takes a reading node name, and either lemmatizes or de-lemmatizes
+it. Returns a list of all readings that are de-lemmatized as a result
+of the toggle.
+
+=cut
+
+sub toggle_reading {
+    my( $self, $rname ) = @_;
+    
+    return unless $rname;
+    my $reading = $self->reading( $rname );
+    if( !$reading || $reading->is_common() ) {
+	# Do nothing, it's a common node.
+	return;
+    } 
+    
+    my $pos = $reading->position;
+    my $old_state = $self->lemmata->{$pos};
+    my @readings_off;
+    if( $old_state && $old_state eq $rname ) {
+	# Turn off the node. We turn on no others by default.
+	push( @readings_off, $reading );
+    } else {
+	# Turn on the node.
+	$self->lemmata->{$pos} = $rname;
+	# Any other 'on' readings in the same position should be off.
+	push( @readings_off, $self->same_position_as( $reading ) );
+	# Any node that is an identical transposed one should be off.
+	push( @readings_off, $reading->identical_readings );
+    }
+    @readings_off = unique_list( @readings_off );
+
+    # Turn off the readings that need to be turned off.
+    my @readings_delemmatized;
+    foreach my $n ( @readings_off ) {
+	my $state = $self->lemmata->{$n->position};
+	if( $state && $state eq $n->name ) { 
+	    # this reading is still on, so turn it off
+	    push( @readings_delemmatized, $n );
+	    my $new_state = undef;
+	    if( $n eq $reading ) {
+		# This is the reading that was clicked, so if there are no
+		# other readings there, turn off the position.  In all other
+		# cases, restore the ellipsis.
+		my @other_n = $self->same_position_as( $n );
+		$new_state = 0 unless @other_n;
+	    }
+	    $self->lemmata->{$n->position} = $new_state;
+	} elsif( $old_state && $old_state eq $n->name ) { 
+	    # another reading has already been turned on here
+	    push( @readings_delemmatized, $n );
+	} # else some other reading was on anyway, so pass.
+    }
+    return @readings_delemmatized;
+}
+
+sub same_position_as {
+    my( $self, $reading ) = @_;
+    my $pos = $reading->position;
+    my @same = grep { $_ ne $reading } $self->readings_at_position( $reading->position );
+    return @same;
+}
+
+# Return the string that joins together a list of witnesses for
+# display on a single path.
+sub path_label {
+    my $self = shift;
+    return join( $self->wit_list_separator, @_ );
+}
+
+sub witnesses_of_label {
+    my( $self, $label ) = @_;
+    my $regex = $self->wit_list_separator;
+    my @answer = split( /\Q$regex\E/, $label );
+    return @answer;
+}    
+
+sub unique_list {
+    my( @list ) = @_;
+    my %h;
+    map { $h{$_->name} = $_ } @list;
+    return values( %h );
+}
+
+sub add_hash_entry {
+    my( $hash, $key, $entry ) = @_;
+    if( exists $hash->{$key} ) {
+	push( @{$hash->{$key}}, $entry );
+    } else {
+	$hash->{$key} = [ $entry ];
+    }
+}
+
 no Moose;
 __PACKAGE__->meta->make_immutable;