X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FCollation.pm;h=7606cc2dfee068c0518c7dcb89bdf744baf7a0d5;hb=e867486f69f12dc06304594022c298935d1c7fb9;hp=fd5bda599b3ca674e37ad8d2bf32306768467eef;hpb=4a8828f0ac801bd0a198cdaf74a7b6769db0ec6b;p=scpubgit%2Fstemmatology.git

diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm
index fd5bda5..7606cc2 100644
--- a/lib/Text/Tradition/Collation.pm
+++ b/lib/Text/Tradition/Collation.pm
@@ -1,28 +1,37 @@
 package Text::Tradition::Collation;
 
+use Encode qw( decode_utf8 );
+use File::Temp;
+use Graph;
 use Graph::Easy;
 use IPC::Run qw( run binary );
+use Text::CSV_XS;
+use Text::Tradition::Collation::Path;
 use Text::Tradition::Collation::Reading;
+use Text::Tradition::Collation::Relationship;
+use XML::LibXML;
 use Moose;
 
 has 'graph' => (
     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',
-	paths => 'edges',
+        add_reading => 'add_node',
+        add_lacuna => 'add_node',
+        del_reading => 'del_node',
+        add_path => 'add_edge',
+        del_path => 'del_edge',
+        reading => 'node',
+        path => 'edge',
+        readings => 'nodes',
+        paths => 'edges',
+        relationships => 'edges',
     },
     default => sub { Graph::Easy->new( undirected => 0 ) },
     );
-		
+                
 
-has 'tradition' => (
+has 'tradition' => (  # TODO should this not be ro?
     is => 'rw',
     isa => 'Text::Tradition',
     );
@@ -34,25 +43,57 @@ has 'svg' => (
     predicate => 'has_svg',
     );
 
-has 'graphviz' => (
+has 'graphml' => (
     is => 'ro',
     isa => 'Str',
-    writer => '_save_graphviz',
-    predicate => 'has_graphviz',
+    writer => '_save_graphml',
+    predicate => 'has_graphml',
     );
 
-has 'graphml' => (
+has 'csv' => (
     is => 'ro',
-    isa => 'XML::LibXML::Document',
-    writer => '_save_graphml',
-    predicate => 'has_graphml',
+    isa => 'Str',
+    writer => '_save_csv',
+    predicate => 'has_csv',
+    );
+
+# 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 => ', ',
-			     );
+    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
@@ -72,14 +113,70 @@ has 'wit_list_separator' => (
 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 );
+    
+	# Start and end points for all texts
+	$self->start( 'INIT' );
+	$self->end( 'INIT' );
 }
 
-# Wrappers around some methods
+around add_lacuna => sub {
+    my $orig = shift;
+    my $self = shift;
+    my $id = shift @_;
+    my $l = $self->$orig( '#LACUNA_' . $id . '#' );
+    $l->is_lacuna( 1 );
+    return $l;
+};
+
+# 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;
+};
+
+# Wrapper around merge_nodes
 sub merge_readings {
     my $self = shift;
     my $first_node = shift;
@@ -89,6 +186,80 @@ sub merge_readings {
     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 relationships between readings.  This is a different
+## sort of graph edge.  Return a success/failure value and a list of
+## node pairs that have been linked.
+
+sub add_relationship {
+    my( $self, $source, $target, $options ) = @_;
+
+    # Make sure there is not another relationship between these two
+    # readings 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 ), $target->edges_to( $source ) ) {
+        if( $rel->class eq 'edge.relationship' ) {
+            return ( undef, "Relationship already exists between these readings" );
+        }
+    }
+    if( $options->{'equal_rank'} && !relationship_valid( $source, $target ) ) {
+        return ( undef, 'Relationship creates witness loop' );
+    }
+
+    # TODO Think about positional hilarity if relationships are added after positions
+    # are assigned.
+    
+    my @joined = ( [ $source->name, $target->name ] );  # Keep track of the nodes we join.
+    
+    $options->{'this_relation'} = [ $source, $target ];
+    my $rel;
+    eval { $rel = Text::Tradition::Collation::Relationship->new( %$options ) };
+    if( $@ ) {
+       return ( undef, $@ );
+    }
+    $self->graph->add_edge( $source, $target, $rel );
+    
+    # TODO Handle global relationship setting
+
+    return( 1, @joined );
+}
+
+sub relationship_valid {
+    my( $source, $target ) = @_;
+    # Check that linking the source and target in a relationship won't lead
+    # to a path loop for any witness.
+    my @proposed_related = ( $source, $target );
+    push( @proposed_related, $source->related_readings );
+    push( @proposed_related, $target->related_readings );
+    my %pr_ids;
+    map { $pr_ids{ $_->name } = 1 } @proposed_related;
+    # The lists of 'in' and 'out' should not have any element that appears
+    # in 'proposed_related'.
+    foreach my $pr ( @proposed_related ) {
+        foreach my $e ( $pr->incoming ) {
+            if( exists $pr_ids{ $e->from->name } ) {
+                return 0;
+            }
+        }
+        foreach my $e ( $pr->outgoing ) {
+            if( exists $pr_ids{ $e->to->name } ) {
+                return 0;
+            }
+        }
+    }
+    return 1;
+}
+
 =head2 Output method(s)
 
 =over
@@ -108,17 +279,66 @@ sub as_svg {
     my( $self, $recalc ) = @_;
     return $self->svg if $self->has_svg;
     
-    $self->_save_graphviz( $self->graph->as_graphviz() )
-	unless( $self->has_graphviz && !$recalc );
+    $self->collapse_graph_paths();
     
     my @cmd = qw/dot -Tsvg/;
     my( $svg, $err );
-    my $in = $self->graphviz;
-    run( \@cmd, \$in, ">", binary(), \$svg );
-    $self->{'svg'} = $svg;
+    my $dotfile = File::Temp->new();
+    ## TODO REMOVE
+    # $dotfile->unlink_on_destroy(0);
+    binmode $dotfile, ':utf8';
+    print $dotfile $self->as_dot();
+    push( @cmd, $dotfile->filename );
+    run( \@cmd, ">", binary(), \$svg );
+    $svg = decode_utf8( $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;
+        $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->name, $reading->label );
+    }
+
+    my @edges = $view eq 'relationship' ? $self->relationships : $self->paths;
+    foreach my $edge ( @edges ) {
+        my %variables = ( 'color' => '#000000',
+                          'fontcolor' => '#000000',
+                          'label' => $edge->label,
+            );
+        my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+        $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
+                         $edge->from->name, $edge->to->name, $varopts );
+    }
+    $dot .= "}\n";
+    return $dot;
+}
+
 =item B<as_graphml>
 
 print $graph->as_graphml( $recalculate )
@@ -138,7 +358,7 @@ sub as_graphml {
     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';
+        'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
 
     # Create the document and root node
     my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
@@ -147,83 +367,312 @@ sub as_graphml {
     $root->setNamespace( $xsi_ns, 'xsi', 0 );
     $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
 
+    # Add the data keys for the graph
+    my %graph_data_keys;
+    my $gdi = 0;
+    my @graph_attributes = qw/ wit_list_separator baselabel linear ac_label /;
+    foreach my $datum ( @graph_attributes ) {
+    	$graph_data_keys{$datum} = 'dg'.$gdi++;
+        my $key = $root->addNewChild( $graphml_ns, 'key' );
+        $key->setAttribute( 'attr.name', $datum );
+        $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
+        $key->setAttribute( 'for', 'graph' );
+        $key->setAttribute( 'id', $graph_data_keys{$datum} );    	
+    }
+
     # Add the data keys for nodes
-    my @node_data = ( 'name', 'token', 'identical', 'position' );
-    foreach my $ndi ( 0 .. $#node_data ) {
-	my $key = $root->addNewChild( $graphml_ns, 'key' );
-	$key->setAttribute( 'attr.name', $node_data[$ndi] );
-	$key->setAttribute( 'attr.type', 'string' );
-	$key->setAttribute( 'for', 'node' );
-	$key->setAttribute( 'id', 'd'.$ndi );
-    }
-
-    # Add the data keys for edges
-    my %wit_hash;
-    my $wit_ctr = 0;
-    foreach my $wit ( $self->getWitnessList ) {
-	my $wit_key = 'w' . $wit_ctr++;
-	$wit_hash{$wit} = $wit_key;
-	my $key = $root->addNewChild( $graphml_ns, 'key' );
-	$key->setAttribute( 'attr.name', $wit );
-	$key->setAttribute( 'attr.type', 'string' );
-	$key->setAttribute( 'for', 'edge' );
-	$key->setAttribute( 'id', $wit_key );
+    my %node_data_keys;
+    my $ndi = 0;
+    foreach my $datum ( qw/ name reading identical rank 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;
+    my @string_keys = qw/ class witness relationship /;
+    my @bool_keys = qw/ extra equal_rank non_correctable non_independent /;
+    foreach my $edge_key( @string_keys ) {
+        $edge_data_keys{$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} );
+    }
+    foreach my $edge_key( @bool_keys ) {
+        $edge_data_keys{$edge_key} = 'de'.$edi++;
+        my $key = $root->addNewChild( $graphml_ns, 'key' );
+        $key->setAttribute( 'attr.name', $edge_key );
+        $key->setAttribute( 'attr.type', 'boolean' );
+        $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( 'id', $self->tradition->name );
     $graph->setAttribute( 'parse.edgeids', 'canonical' );
-    $graph->setAttribute( 'parse.edges', $self->edges() );
+    $graph->setAttribute( 'parse.edges', scalar($self->paths) );
     $graph->setAttribute( 'parse.nodeids', 'canonical' );
-    $graph->setAttribute( 'parse.nodes', $self->nodes() );
+    $graph->setAttribute( 'parse.nodes', scalar($self->readings) );
     $graph->setAttribute( 'parse.order', 'nodesfirst' );
+    
+    # Collation attribute data
+    foreach my $datum ( @graph_attributes ) {
+		_add_graphml_data( $graph, $graph_data_keys{$datum}, $self->$datum );
+	}
 
     my $node_ctr = 0;
     my %node_hash;
-    foreach my $n ( $self->readings ) {
-	my %this_node_data = ();
-	foreach my $ndi ( 0 .. $#node_data ) {
-	    my $value;
-	    $this_node_data{'d'.$ndi} = $n->name if $node_data[$ndi] eq 'name';
-	    $this_node_data{'d'.$ndi} = $n->label 
-		if $node_data[$ndi] eq 'token';
-	    $this_node_data{'d'.$ndi} = $n->primary->name if $n->has_primary;
-	    $this_node_data{'d'.$ndi} = 
-		$self->{'positions'}->node_position( $n )
-		if $node_data[$ndi] eq 'position';
-	}
-	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 );
-	    
-	foreach my $dk ( keys %this_node_data ) {
-	    my $d_el = $node_el->addNewChild( $graphml_ns, 'data' );
-	    $d_el->setAttribute( 'key', $dk );
-	    $d_el->appendTextChild( $this_node_data{$dk} );
-	}
+    # 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{'rank'}, $n->rank )
+            if $n->has_rank;
+        _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 && $n->primary ne $n;
     }
 
-    foreach my $e ( $self->edges() ) {
-	my( $name, $from, $to ) = ( $e->name,
-				    $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 );
-	# TODO Got to add the witnesses
+    # Add the path and relationship 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 );
+        
+        # For some classes we have extra information to save.
+        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'};
+            # Is this an ante-corr witness?
+            my $aclabel = $self->ac_label;
+            if( $e->label =~ /^(.*)\Q$aclabel\E$/ ) {
+            	# Keep the base witness
+                $base = $1;
+                # ...and record that this is an 'extra' reading path
+                _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, 'true' );
+            }
+            _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
+        } elsif( $e->sub_class eq 'relationship' ) {
+            # It's a relationship, so save the relationship data
+            _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $e->label );
+            _add_graphml_data( $edge_el, $edge_data_keys{'equal_rank'}, $e->equal_rank );
+            _add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'}, $e->non_correctable );
+            _add_graphml_data( $edge_el, $edge_data_keys{'non_independent'}, $e->non_independent );
+        } 
     }
 
-    # Return the thing
-    $self->_save_graphml( $graphml );
-    return $graphml;
+    # Save and return the thing
+    my $result = decode_utf8( $graphml->toString(1) );
+    $self->_save_graphml( $result );
+    return $result;
+}
+
+sub _add_graphml_data {
+    my( $el, $key, $value ) = @_;
+    return unless defined $value;
+    my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
+    $data_el->setAttribute( 'key', $key );
+    $data_el->appendText( $value );
+}
+
+=item B<as_csv>
+
+print $graph->as_csv( $recalculate )
+
+Returns a CSV alignment table representation of the collation graph, one
+row per witness (or witness uncorrected.) Unless $recalculate is passed
+(and is a true value), the method will return a cached copy of the CSV
+after the first call to the method.
+
+=cut
+
+sub as_csv {
+    my( $self, $recalc ) = @_;
+    return $self->csv if $self->has_csv;
+    my $table = $self->make_alignment_table;
+    my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );    
+    my @result;
+    foreach my $row ( @$table ) {
+        $csv->combine( @$row );
+        push( @result, decode_utf8( $csv->string ) );
+    }
+    $self->_save_csv( join( "\n", @result ) );
+    return $self->csv;
+}
+
+# Make an alignment table - $noderefs controls whether the objects
+# in the table are the nodes or simply their readings.
+
+sub make_alignment_table {
+    my( $self, $noderefs ) = @_;
+    unless( $self->linear ) {
+        warn "Need a linear graph in order to make an alignment table";
+        return;
+    }
+    my $table;
+    my @all_pos = sort { $a <=> $b } $self->possible_positions;
+    foreach my $wit ( $self->tradition->witnesses ) {
+        # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
+        my @row = _make_witness_row( $wit->path, \@all_pos, $noderefs );
+        unshift( @row, $wit->sigil );
+        push( @$table, \@row );
+        if( $wit->has_ante_corr ) {
+            my @ac_row = _make_witness_row( $wit->uncorrected_path, \@all_pos, $noderefs );
+            unshift( @ac_row, $wit->sigil . $self->ac_label );
+            push( @$table, \@ac_row );
+        }           
+    }
+
+    # Return a table where the witnesses read in columns rather than rows.
+    my $turned = _turn_table( $table );
+    return $turned;
+}
+
+sub _make_witness_row {
+    my( $path, $positions, $noderefs ) = @_;
+    my %char_hash;
+    map { $char_hash{$_} = undef } @$positions;
+    foreach my $rdg ( @$path ) {
+        my $rtext = $rdg->text;
+        $rtext = '#LACUNA#' if $rdg->is_lacuna;
+        $char_hash{$rdg->rank} = $noderefs ? $rdg : $rtext;
+    }
+    my @row = map { $char_hash{$_} } @$positions;
+    # Fill in lacuna markers for undef spots in the row
+    my $last_el = shift @row;
+    my @filled_row = ( $last_el );
+    foreach my $el ( @row ) {
+        # If we are using node reference, make the lacuna node appear many times
+        # in the table.  If not, use the lacuna tag.
+        if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
+            $el = $noderefs ? $last_el : '#LACUNA#';
+        }
+        push( @filled_row, $el );
+        $last_el = $el;
+    }
+    return @filled_row;
+}
+
+# Tiny utility function to say if a table element is a lacuna
+sub _el_is_lacuna {
+    my $el = shift;
+    return 1 if $el eq '#LACUNA#';
+    return 1 if ref( $el ) eq 'Text::Tradition::Collation::Reading'
+        && $el->is_lacuna;
+    return 0;
+}
+
+# Helper to turn the witnesses along columns rather than rows.  Assumes
+# equal-sized rows.
+sub _turn_table {
+    my( $table ) = @_;
+    my $result = [];
+    return $result unless scalar @$table;
+    my $nrows = scalar @{$table->[0]};
+    foreach my $idx ( 0 .. $nrows - 1 ) {
+        foreach my $wit ( 0 .. $#{$table} ) {
+            $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
+        }
+    }
+    return $result;        
+}
+
+
+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 $label;
+            my @compressed_wits = @{$newlabels->{$newdest}};
+            if( @compressed_wits < $majority ) {
+                $label = join( ', ', sort( @{$newlabels->{$newdest}} ) );
+            } else {
+                ## TODO FIX THIS HACK
+                my @aclabels;
+                foreach my $wit ( @compressed_wits ) {
+                    push( @aclabels, $wit ) if( $wit =~ /^(.*?)(\s*\(?a\.\s*c\.\)?)$/ );
+                }
+                $label = join( ', ', 'majority', sort( @aclabels ) );
+            }
+            
+            my $newpath = $self->add_path( $node, $self->reading( $newdest ), $label );
+            $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;
+        warn sprintf( "No hidden witnesses on %s -> %s ?", $from->name, $to->name )
+            unless $path->has_hidden_witnesses;
+        my @wits = @{$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();
@@ -234,13 +683,90 @@ Returns the beginning of the collation, a meta-reading with label '#START#'.
 
 sub start {
     # Return the beginning reading of the graph.
+    my( $self, $new_start ) = @_;
+    my $start = $self->reading( '#START#' );
+    if( ref( $new_start ) eq 'Text::Tradition::Collation::Reading' ) {
+    	# Replace the existing start node.
+        $self->del_reading( '#START#' );
+        $self->graph->rename_node( $new_start, '#START#' );
+        $start = $new_start;
+    } elsif ( $new_start && $new_start eq 'INIT' ) {
+    	# Make a new start node.
+    	$start = $self->add_reading( '#START#' );
+    }
+    # Make sure the start node is a meta node
+    $start->is_meta( 1 );
+    # Make sure the start node has a start position.
+    unless( $start->has_rank ) {
+        $start->rank( '0' );
+    }
+    return $start;
+}
+
+=item B<end>
+
+my $end = $collation->end();
+
+Returns the end of the collation, a meta-reading with label '#END#'.
+
+=cut
+
+sub end {
     my $self = shift;
-    my( $new_start ) = @_;
-    if( $new_start ) {
-	$self->del_reading( '#START#' );
-	$self->graph->rename_node( $new_start, '#START#' );
+    my( $new_end ) = @_;
+    my $end = $self->reading( '#END#' );
+    if( ref( $new_end ) eq 'Text::Tradition::Collation::Reading' ) {
+        $self->del_reading( '#END#' );
+        $self->graph->rename_node( $new_end, '#END#' );
+        $end = $new_end
+    } elsif ( $new_end && $new_end eq 'INIT' ) {
+    	# Make a new start node.
+    	$end = $self->add_reading( '#END#' );
     }
-    return $self->reading('#START#');
+    # Make sure the start node is a meta node
+    $end->is_meta( 1 );
+    return $end;
+}
+
+=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
+
+# TODO Think about returning some lazy-eval iterator.
+
+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>
@@ -248,12 +774,12 @@ sub start {
 my $next_reading = $graph->next_reading( $reading, $witpath );
 
 Returns the reading that follows the given reading along the given witness
-path.  TODO These are badly named.
+path.  
 
 =cut
 
 sub next_reading {
-    # Return the successor via the corresponding edge.
+    # Return the successor via the corresponding path.
     my $self = shift;
     return $self->_find_linked_reading( 'next', @_ );
 }
@@ -263,172 +789,463 @@ sub next_reading {
 my $prior_reading = $graph->prior_reading( $reading, $witpath );
 
 Returns the reading that precedes the given reading along the given witness
-path.  TODO These are badly named.
+path.  
 
 =cut
 
 sub prior_reading {
-    # Return the predecessor via the corresponding edge.
+    # Return the predecessor via the corresponding path.
     my $self = shift;
     return $self->_find_linked_reading( 'prior', @_ );
 }
 
 sub _find_linked_reading {
-    my( $self, $direction, $node, $edge ) = @_;
-    $edge = 'base text' unless $edge;
-    my @linked_edges = $direction eq 'next' 
-	? $node->outgoing() : $node->incoming();
-    return undef unless scalar( @linked_edges );
+    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 edge that contains all of the
-    # witnesses supplied in $edge.
-    my @edge_wits = $self->witnesses_of_label( $edge );
-    foreach my $le ( @linked_edges ) {
-	my @le_wits = $self->witnesses_of_label( $le->name );
-	if( _is_within( \@edge_wits, \@le_wits ) ) {
-	    # This is the right edge.
-	    return $direction eq 'next' ? $le->to() : $le->from();
-	}
+    # 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 edge $edge";
+        . " along path $path";
     return undef;
 }
 
 # Some set logic.
 sub _is_within {
     my( $set1, $set2 ) = @_;
-    my $ret = 1;
+    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;
+        $ret = 0 unless grep { /^\Q$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.
+# that the graph has in common.  If $using_base is true, some 
+# different logic is needed.
+# NOTE This does not create paths; it merely finds common readings.
 
 sub walk_witness_paths {
-    my( $self, $end ) = @_;
+    my( $self ) = @_;
     # 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_nodes;
-    foreach my $wit ( @{$self->tradition->witnesses} ) {
-	my $curr_reading = $self->start;
-	my @wit_path = ( $curr_reading );
-	my %seen_readings;
-	# TODO Detect loops at some point
-	while( $curr_reading->name ne $end->name ) {
-	    if( $seen_readings{$curr_reading->name} ) {
-		warn "Detected loop walking path for witness " . $wit->sigil
-		    . " at reading " . $curr_reading->name;
-		last;
-	    }
-	    my $next_reading = $self->next_reading( $curr_reading, 
-						    $wit->sigil );
-	    push( @wit_path, $next_reading );
-	    $seen_readings{$curr_reading->name} = 1;
-	    $curr_reading = $next_reading;
-	}
-	$wit->path( \@wit_path );
-	if( @common_nodes ) {
-	    my @cn;
-	    foreach my $n ( @wit_path ) {
-		push( @cn, $n ) if grep { $_ eq $n } @common_nodes;
-	    }
-	    @common_nodes = ();
-	    push( @common_nodes, @cn );
-	} else {
-	    push( @common_nodes, @wit_path );
-	}
+    my @common_readings;
+    foreach my $wit ( $self->tradition->witnesses ) {
+        my $curr_reading = $self->start;
+        my @wit_path = $self->reading_sequence( $self->start, $self->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_nodes ) {
-	print STDERR "Setting " . $cn->name . " as common node\n";
-	$cn->make_common;
+    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;
+        $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;
+}
+
+
+# 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 ) = @_;
+    foreach my $wit ( $self->tradition->witnesses ) {
+        print STDERR "Making path for " . $wit->sigil . "\n";
+        $self->make_witness_path( $wit );
+    }
+}
+
+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 );
+    }
+    if( $wit->has_ante_corr ) {
+        @chain = @{$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 calculate_ranks {
+    my $self = shift;
+    # Walk a version of the graph where every node linked by a relationship 
+    # edge is fundamentally the same node, and do a topological ranking on
+    # the nodes in this graph.
+    my $topo_graph = Graph->new();
+    my %rel_containers;
+    my $rel_ctr = 0;
+    # Add the nodes
+    foreach my $r ( $self->readings ) {
+        next if exists $rel_containers{$r->name};
+        my @rels = $r->related_readings( 'colocated' );
+        if( @rels ) {
+            # Make a relationship container.
+            push( @rels, $r );
+            my $rn = 'rel_container_' . $rel_ctr++;
+            $topo_graph->add_vertex( $rn );
+            foreach( @rels ) {
+                $rel_containers{$_->name} = $rn;
+            }
+        } else {
+            # Add a new node to mirror the old node.
+            $rel_containers{$r->name} = $r->name;
+            $topo_graph->add_vertex( $r->name );
+        }
+    }
+
+    # Add the edges. Need only one edge between any pair of nodes.
+    foreach my $r ( $self->readings ) {
+        foreach my $n ( $r->neighbor_readings( 'forward' ) ) {
+        	my( $tfrom, $tto ) = ( $rel_containers{$r->name},
+        		$rel_containers{$n->name} );
+            $topo_graph->add_edge( $tfrom, $tto )
+            	unless $topo_graph->has_edge( $tfrom, $tto );
+        }
+    }
+    
+    # Now do the rankings, starting with the start node.
+    my $topo_start = $rel_containers{$self->start->name};
+    my $node_ranks = { $topo_start => 0 };
+    my @curr_origin = ( $topo_start );
+    # A little iterative function.
+    while( @curr_origin ) {
+        @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
+    }
+    # Transfer our rankings from the topological graph to the real one.
+    foreach my $r ( $self->readings ) {
+        $r->rank( $node_ranks->{$rel_containers{$r->name}} );
+    }
+}
+
+sub _assign_rank {
+    my( $graph, $node_ranks, @current_nodes ) = @_;
+    # Look at each of the children of @current_nodes.  If all the child's 
+    # parents have a rank, assign it the highest rank + 1 and add it to 
+    # @next_nodes.  Otherwise skip it; we will return when the highest-ranked
+    # parent gets a rank.
+    my @next_nodes;
+    foreach my $c ( @current_nodes ) {
+        warn "Current reading $c has no rank!"
+            unless exists $node_ranks->{$c};
+        # print STDERR "Looking at child of node $c, rank " 
+        #     . $node_ranks->{$c} . "\n";
+        foreach my $child ( $graph->successors( $c ) ) {
+            next if exists $node_ranks->{$child};
+            my $highest_rank = -1;
+            my $skip = 0;
+            foreach my $parent ( $graph->predecessors( $child ) ) {
+                if( exists $node_ranks->{$parent} ) {
+                    $highest_rank = $node_ranks->{$parent} 
+                        if $highest_rank <= $node_ranks->{$parent};
+                } else {
+                    $skip = 1;
+                    last;
+                }
+            }
+            next if $skip;
+            my $c_rank = $highest_rank + 1;
+            # print STDERR "Assigning rank $c_rank to node $child \n";
+            $node_ranks->{$child} = $c_rank;
+            push( @next_nodes, $child );
+        }
+    }
+    return @next_nodes;
+}
+
+# Another method to make up for rough collation methods.  If the same reading
+# appears multiple times at the same rank, collapse the nodes.
+sub flatten_ranks {
+    my $self = shift;
+    my %unique_rank_rdg;
+    foreach my $rdg ( $self->readings ) {
+        next unless $rdg->has_rank;
+        my $key = $rdg->rank . "||" . $rdg->text;
+        if( exists $unique_rank_rdg{$key} ) {
+            # Combine!
+            print STDERR "Combining readings at same rank: $key\n";
+            $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
+        } else {
+            $unique_rank_rdg{$key} = $rdg;
+        }
+    }
+}
+
+
+sub possible_positions {
+    my $self = shift;
+    my %all_pos;
+    map { $all_pos{ $_->rank } = 1 } $self->readings;
+    return keys %all_pos;
+}
+
+# TODO think about indexing this.
+sub readings_at_position {
+    my( $self, $position, $strict ) = @_;
+    my @answer;
+    foreach my $r ( $self->readings ) {
+        push( @answer, $r ) if $r->is_at_position( $position, $strict );
+    }
+    return @answer;
+}
+
+## Lemmatizer functions
+
+sub init_lemmata {
+    my $self = shift;
+
+    foreach my $position ( $self->possible_positions ) {
+        $self->lemmata->{$position} = undef;
+    }
+
+    foreach my $cr ( $self->common_readings ) {
+        $self->lemmata->{$cr->position->maxref} = $cr->name;
     }
 }
 
 sub common_readings {
     my $self = shift;
     my @common = grep { $_->is_common } $self->readings();
-    return @common;
+    return sort { $a->rank <=> $b->rank } @common;
 }
+    
+=item B<lemma_readings>
 
-# Calculate the relative positions of nodes in the graph, if they
-# were not given to us.
-sub calculate_positions {
-    my $self = shift;
+my @state = $graph->lemma_readings( @readings_delemmatized );
 
-    # 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 @common = $self->common_readings();
-
-    my $node_pos = {};
-    foreach my $wit ( @{$self->tradition->witnesses} ) {
-	# First we walk each path, making a matrix for each 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 $wn ( @{$wit->path} ) {
-	    if( $wn eq $common[$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.
-	    }
-	}
+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->reference } = $_->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.  The lemmata hash
+    # should contain fixed positions, range positions whose node was
+    # just turned off, and range positions whose node is on.
+    my @answer;
+    my %fixed_positions;
+    # TODO One of these is probably redundant.
+    map { $fixed_positions{$_} = 0 } keys %{$self->lemmata};
+    map { $fixed_positions{$_} = 0 } keys %{$positions_off};
+    map { $fixed_positions{$_} = 1 } $self->possible_positions;
+    foreach my $pos ( sort { Text::Tradition::Collation::Position::str_cmp( $a, $b ) } keys %fixed_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 = undef;
+        $active = $self->lemmata->{$pos} if exists $self->lemmata->{$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 {
+                unless( $fixed_positions{$pos} ) {
+                    $active = 0;
+                    delete $self->lemmata->{$pos};
+                }
+                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} ] );
+            delete $self->lemmata->{$pos} unless $fixed_positions{$pos};
+        }
     }
+
+    return @answer;
 }
 
-sub _cmp_position {
-    my( $a, $b ) = @_;
-    my @pos_a = split(/,/, $a );
-    my @pos_b = split(/,/, $b );
+=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 $fixed = $reading->position->fixed;
+    my $old_state = $self->lemmata->{$pos->reference};
+
+    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->reference} = $rname;
+        # Any other 'on' readings in the same position should be off
+        # if we have a fixed position.
+        push( @readings_off, $self->same_position_as( $reading, 1 ) )
+            if $pos->fixed;
+        # 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 $npos = $n->position;
+        my $state = undef;
+        $state = $self->lemmata->{$npos->reference}
+            if defined $self->lemmata->{$npos->reference};
+        if( $state && $state eq $n->name ) { 
+            # this reading is still on, so turn it off
+            push( @readings_delemmatized, $n );
+            my $new_state = undef;
+            if( $npos->fixed && $n eq $reading ) {
+                # This is the reading that was clicked, so if there are no
+                # other readings there and this is a fixed position, turn off 
+                # the position.  In all other cases, restore the ellipsis.
+                my @other_n = $self->same_position_as( $n ); # TODO do we need strict?
+                $new_state = 0 unless @other_n;
+            }
+            $self->lemmata->{$npos->reference} = $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;
+}
 
-    my $big_cmp = $pos_a[0] <=> $pos_b[0];
-    return $big_cmp if $big_cmp;
-    # else 
-    return $pos_a[1] <=> $pos_b[1];
+sub same_position_as {
+    my( $self, $reading, $strict ) = @_;
+    my $pos = $reading->position;
+    my %onpath = ( $reading->name => 1 );
+    # TODO This might not always be sufficient.  We really want to
+    # exclude all readings on this one's path between its two
+    # common points.
+    map { $onpath{$_->name} = 1 } $reading->neighbor_readings;
+    my @same = grep { !$onpath{$_->name} } 
+        $self->readings_at_position( $reading->position, $strict );
+    return @same;
 }
- 
+
 # Return the string that joins together a list of witnesses for
 # display on a single path.
 sub path_label {
@@ -437,10 +1254,37 @@ sub path_label {
 }
 
 sub witnesses_of_label {
-    my $self = shift;
+    my( $self, $label ) = @_;
     my $regex = $self->wit_list_separator;
-    return split( /^\Q$regex\E$/, @_ );
+    my @answer = split( /\Q$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;
+
+=head1 BUGS / TODO
+
+=over
+
+=item * Rationalize edge classes
+
+=item * Port the internal graph from Graph::Easy to Graph
+
+=back