X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FCollation.pm;h=85c23603cd5a7e79ab8832532b3b7cfbb7fd0267;hb=0e47f4f67650eaa804f9e23b3241718d8eb94433;hp=dd60f0cf1fa23d3dc9732c0824025e2f7014e273;hpb=b5054ca9a01f0751d7b00cf1ed98e2fa0f8c73ab;p=scpubgit%2Fstemmatology.git

diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm
index dd60f0c..85c2360 100644
--- a/lib/Text/Tradition/Collation.pm
+++ b/lib/Text/Tradition/Collation.pm
@@ -1,56 +1,52 @@
 package Text::Tradition::Collation;
 
-use Graph::Easy;
+use Encode qw( decode_utf8 );
+use File::Temp;
+use Graph;
 use IPC::Run qw( run binary );
+use Text::CSV_XS;
 use Text::Tradition::Collation::Reading;
-use Text::Tradition::Collation::Path;
+use Text::Tradition::Collation::RelationshipStore;
 use XML::LibXML;
 use Moose;
 
-has 'graph' => (
+has 'sequence' => (
     is => 'ro',
-    isa => 'Graph::Easy',
+    isa => 'Graph',
+    default => sub { Graph->new() },
     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',
-	relationships => 'edges',
+    	paths => 'edges',
     },
-    default => sub { Graph::Easy->new( undirected => 0 ) },
     );
-		
+    
+has 'relations' => (
+	is => 'ro',
+	isa => 'Text::Tradition::Collation::RelationshipStore',
+	handles => {
+		relationships => 'relationships',
+		related_readings => 'related_readings',
+	},
+	writer => '_set_relations',
+	);
 
 has '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',
+    isa => 'Text::Tradition',
+    weak_ref => 1,
     );
 
-# 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]]',
+has 'readings' => (
+	isa => 'HashRef[Text::Tradition::Collation::Reading]',
+	traits => ['Hash'],
+    handles => {
+        reading     => 'get',
+        _add_reading => 'set',
+        del_reading => 'delete',
+        has_reading => 'exists',
+        readings   => 'values',
+    },
     default => sub { {} },
-    );
+	);
 
 has 'wit_list_separator' => (
     is => 'rw',
@@ -64,17 +60,31 @@ has 'baselabel' => (
     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.)',
+    );
+    
+has 'start' => (
+	is => 'ro',
+	isa => 'Text::Tradition::Collation::Reading',
+	writer => '_set_start',
+	weak_ref => 1,
+	);
+
+has 'end' => (
+	is => 'ro',
+	isa => 'Text::Tradition::Collation::Reading',
+	writer => '_set_end',
+	weak_ref => 1,
+	);
 
 # The collation can be created two ways:
 # 1. Collate a set of witnesses (with CollateX I guess) and process
@@ -92,110 +102,181 @@ has 'linear' => (
 # 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 );
+    my $self = shift;
+    $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
+    $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
+    $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
 }
 
-# Wrapper around add_path 
+### Reading construct/destruct functions
 
-around add_path => sub {
-    my $orig = shift;
-    my $self = shift;
+sub add_reading {
+	my( $self, $reading ) = @_;
+	unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
+		my %args = %$reading;
+		$reading = Text::Tradition::Collation::Reading->new( 
+			'collation' => $self,
+			%args );
+	}
+	# First check to see if a reading with this ID exists.
+	if( $self->reading( $reading->id ) ) {
+		warn "Collation already has a reading with id " . $reading->id;
+		return undef;
+	}
+	$self->_add_reading( $reading->id => $reading );
+	# Once the reading has been added, put it in both graphs.
+	$self->sequence->add_vertex( $reading->id );
+	$self->relations->add_reading( $reading->id );
+	return $reading;
+};
 
-    # 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
-    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 ) {
-	    return;
+around del_reading => sub {
+	my $orig = shift;
+	my $self = shift;
+	my $arg = shift;
+	
+	if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
+		$arg = $arg->id;
 	}
-    }
-    # Do the deed
-    $self->$orig( @_ );
+	# Remove the reading from the graphs.
+	$self->sequence->delete_vertex( $arg );
+	$self->relations->delete_reading( $arg );
+	
+	# Carry on.
+	$self->$orig( $arg );
 };
 
-# Wrapper around paths
-around paths => sub {
-    my $orig = shift;
-    my $self = shift;
+# merge_readings( $main, $to_be_deleted );
 
-    my @result = grep { $_->class eq 'edge.path' } $self->$orig( @_ );
-    return @result;
-};
+sub merge_readings {
+	my $self = shift;
+
+	# We only need the IDs for adding paths to the graph, not the reading
+	# objects themselves.
+    my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
+
+    # The kept reading should inherit the paths and the relationships
+    # of the deleted reading.
+	foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
+		my @vector = ( $kept );
+		push( @vector, $path->[1] ) if $path->[0] eq $deleted;
+		unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
+		next if $vector[0] eq $vector[1]; # Don't add a self loop
+		my %wits = %{$self->sequence->get_edge_attributes( @$path )};
+		$self->sequence->add_edge( @vector );
+		my $fwits = $self->sequence->get_edge_attributes( @vector );
+		@wits{keys %$fwits} = values %$fwits;
+		$self->sequence->set_edge_attributes( @vector, \%wits );
+	}
+	$self->relations->merge_readings( $kept, $deleted, $combine_char );
+	
+	# Do the deletion deed.
+	if( $combine_char ) {
+		my $kept_obj = $self->reading( $kept );
+		my $new_text = join( $combine_char, $kept_obj->text, 
+			$self->reading( $deleted )->text );
+		$kept_obj->alter_text( $new_text );
+	}
+	$self->del_reading( $deleted );
+}
 
-around relationships => sub {
-    my $orig = shift;
-    my $self = shift;
-    my @result = grep { $_->class eq 'edge.relationship' } $self->$orig( @_ );
-    return @result;
+
+# Helper function for manipulating the graph.
+sub _stringify_args {
+	my( $self, $first, $second, $arg ) = @_;
+    $first = $first->id
+        if ref( $first ) eq 'Text::Tradition::Collation::Reading';
+    $second = $second->id
+        if ref( $second ) eq 'Text::Tradition::Collation::Reading';        
+    return( $first, $second, $arg );
+}
+
+### Path logic
+
+sub add_path {
+	my $self = shift;
+
+	# We only need the IDs for adding paths to the graph, not the reading
+	# objects themselves.
+    my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+
+	# Connect the readings
+    $self->sequence->add_edge( $source, $target );
+    # Note the witness in question
+    $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
 };
 
-# Wrapper around merge_nodes
+sub del_path {
+	my $self = shift;
+	my @args;
+	if( ref( $_[0] ) eq 'ARRAY' ) {
+		my $e = shift @_;
+		@args = ( @$e, @_ );
+	} else {
+		@args = @_;
+	}
 
-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( @_ );
+	# We only need the IDs for adding paths to the graph, not the reading
+	# objects themselves.
+    my( $source, $target, $wit ) = $self->_stringify_args( @args );
+
+	if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
+		$self->sequence->delete_edge_attribute( $source, $target, $wit );
+	}
+	unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
+		$self->sequence->delete_edge( $source, $target );
+	}
 }
 
+
 # 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 @paths;
+	my $self = shift;
+    my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+	return undef unless $self->sequence->has_edge( $source, $target );
+	return $self->sequence->has_edge_attribute( $source, $target, $wit );
 }
 
-## Dealing with relationships between readings.  This is a different
-## sort of graph edge.
+=head2 add_relationship( $reading1, $reading2, $definition )
+
+Adds the specified relationship between the two readings.  A relationship
+is transitive (i.e. undirected); the options for its definition may be found
+in Text::Tradition::Collation::Relationship.
+
+=cut
+
+# Wouldn't it be lovely if edges could be objects, and all this type checking
+# and attribute management could be done via Moose?
 
 sub add_relationship {
-    my( $self, $type, $source, $target, $global ) = @_;
-    my $rel = Text::Tradition::Collation::Relationship->new(
-	    'sort' => $type,
-	    'global' => $global,
-	    'orig_relation' => [ $source, $target ],
-    );
-    print STDERR sprintf( "Setting relationship %s between readings %s (%s)"
-			  . " and %s (%s)\n", $type, 
-			  $source->label, $source->name,
-			  $target->label, $target->name );
-    $self->graph->add_edge( $source, $target, $rel );
-    if( $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(
-		    'sort' => $type,
-		    'global' => $global,
-		    'orig_relation' => [ $source, $target ],
-		    );
-		$self->graph->add_edge( $r, $colocated[0], $dup_rel );
-	    }
+	my $self = shift;
+    my( $source, $target, $opts ) = $self->_stringify_args( @_ );
+    my( $ret, @vectors ) = $self->relations->add_relationship( $source, 
+    	$self->reading( $source ), $target, $self->reading( $target ), $opts );
+    # Force a full rank recalculation every time. Yuck.
+    $self->calculate_ranks() if $ret && $self->end->has_rank;
+    return( $ret, @vectors );
+}
+
+=head2 reading_witnesses( $reading )
+
+Return a list of sigils corresponding to the witnesses in which the reading appears.
+
+=cut
+
+sub reading_witnesses {
+	my( $self, $reading ) = @_;
+	# We need only check either the incoming or the outgoing edges; I have
+	# arbitrarily chosen "incoming".  Thus, special-case the start node.
+	if( $reading eq $self->start ) {
+		return map { $_->sigil } $self->tradition->witnesses;
 	}
-    }
+	my %all_witnesses;
+	foreach my $e ( $self->sequence->edges_to( $reading ) ) {
+		my $wits = $self->sequence->get_edge_attributes( @$e );
+		@all_witnesses{ keys %$wits } = 1;
+	}
+	return keys %all_witnesses;
 }
 
 =head2 Output method(s)
@@ -204,33 +285,63 @@ sub add_relationship {
 
 =item B<as_svg>
 
-print $graph->as_svg( $recalculate );
+print $collation->as_svg();
 
-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.
+Returns an SVG string that represents the graph, via as_dot and graphviz.
 
 =cut
 
 sub as_svg {
-    my( $self, $recalc ) = @_;
-    return $self->svg if $self->has_svg;
+    my( $self ) = @_;
+        
+    my @cmd = qw/dot -Tsvg/;
+    my( $svg, $err );
+    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 );
+    return $svg;
+}
+
+=item B<svg_subgraph>
+
+print $collation->svg_subgraph( $from, $to )
+
+Returns an SVG string that represents the portion of the graph given by the
+specified range.  The $from and $to variables refer to ranks within the graph.
+
+=cut
+
+sub svg_subgraph {
+    my( $self, $from, $to ) = @_;
     
-    $self->collapse_graph_paths();
+    my $dot = $self->as_dot( $from, $to );
+    unless( $dot ) {
+    	warn "Could not output a graph with range $from - $to";
+    	return;
+    }
     
     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();
+    my $dotfile = File::Temp->new();
+    ## TODO REMOVE
+    # $dotfile->unlink_on_destroy(0);
+    binmode $dotfile, ':utf8';
+    print $dotfile $dot;
+    push( @cmd, $dotfile->filename );
+    run( \@cmd, ">", binary(), \$svg );
+    $svg = decode_utf8( $svg );
     return $svg;
 }
 
+
 =item B<as_dot>
 
-print $graph->as_dot( $view, $recalculate );
+print $collation->as_dot();
 
 Returns a string that is the collation graph expressed in dot
 (i.e. GraphViz) format.  The 'view' argument determines what kind of
@@ -242,33 +353,116 @@ graph is produced.
 =cut
 
 sub as_dot {
-    my( $self, $view ) = @_;
-    $view = 'path' unless $view;
+    my( $self, $startrank, $endrank ) = @_;
+    
+    # Check the arguments
+    if( $startrank ) {
+    	return if $endrank && $startrank > $endrank;
+    	return if $startrank > $self->end->rank;
+	}
+	if( defined $endrank ) {
+		return if $endrank < 0;
+		$endrank = undef if $endrank == $self->end->rank;
+	}
+	
     # TODO consider making some of these things configurable
-    my $dot = sprintf( "digraph %s {\n", $self->tradition->name );
+    my $graph_name = $self->tradition->name;
+    $graph_name =~ s/[^\w\s]//g;
+    $graph_name = join( '_', split( /\s+/, $graph_name ) );
+    my $dot = sprintf( "digraph %s {\n", $graph_name );
     $dot .= "\tedge [ arrowhead=open ];\n";
-    $dot .= "\tgraph [ rankdir=LR ];\n";
+    $dot .= "\tgraph [ rankdir=LR,bgcolor=none ];\n";
     $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
-		     11, "white", "filled", $self->graph->get_attribute( 'node', 'shape' ) );
+                     11, "white", "filled", "ellipse" );
 
+	# Output substitute start/end readings if necessary
+	if( $startrank ) {
+		$dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
+	}
+	if( $endrank ) {
+		$dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";	
+	}
+	my %used;  # Keep track of the readings that actually appear in the graph
+	my %subedges;
+	my %subend;
     foreach my $reading ( $self->readings ) {
-	next if $reading->name eq $reading->label;
-	$dot .= sprintf( "\t\"%s\" [ label=\"%s\" ]\n", $reading->name, $reading->label );
+    	# Only output readings within our rank range.
+    	next if $startrank && $reading->rank < $startrank;
+    	next if $endrank && $reading->rank > $endrank;
+        $used{$reading->id} = 1;
+        $subedges{$reading->id} = '#SUBSTART#' 
+        	if $startrank && $startrank == $reading->rank;
+        $subedges{$reading->id} = '#SUBEND#' 
+        	if $endrank && $endrank == $reading->rank;
+        # Need not output nodes without separate labels
+        next if $reading->id eq $reading->text;
+        my $label = $reading->text;
+        $label =~ s/\"/\\\"/g;
+        $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
     }
-
-    my @edges = $view eq 'relationship' ? $self->relationships : $self->paths;
+    
+    # Add substitute start and end edges if necessary
+    foreach my $node ( keys %subedges ) {
+		my @vector = ( $subedges{$node}, $node );
+		@vector = reverse( @vector ) if $vector[0] =~ /END/;
+    	my $witstr = join( ', ', sort $self->reading_witnesses( $self->reading( $node ) ) );
+    	my %variables = ( 'color' => '#000000',
+                          'fontcolor' => '#000000',
+                          'label' => $witstr,
+            );
+        my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+		$dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n", @vector, $varopts );
+	}
+	
+	# Add the real edges
+    my @edges = $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 );
+    	# Do we need to output this edge?
+    	if( $used{$edge->[0]} && $used{$edge->[1]} ) {;
+			my %variables = ( 'color' => '#000000',
+							  'fontcolor' => '#000000',
+							  'label' => join( ', ', $self->path_display_label( $edge ) ),
+				);
+			my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+			# Account for the rank gap if necessary
+			my $rankgap = $self->reading( $edge->[1] )->rank 
+				- $self->reading( $edge->[0] )->rank;
+			$varopts .= ", minlen=$rankgap" if $rankgap > 1;
+			$dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
+							 $edge->[0], $edge->[1], $varopts );
+        }
     }
-
+    
     $dot .= "}\n";
     return $dot;
 }
 
+sub path_witnesses {
+	my( $self, @edge ) = @_;
+	# If edge is an arrayref, cope.
+	if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
+		my $e = shift @edge;
+		@edge = @$e;
+	}
+	my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
+	return sort @wits;
+}
+
+sub path_display_label {
+	my( $self, $edge ) = @_;
+	my @wits = $self->path_witnesses( $edge );
+	my $maj = scalar( $self->tradition->witnesses ) * 0.6;
+	if( scalar @wits > $maj ) {
+		return 'majority';
+	} else {
+		return join( ', ', @wits );
+	}
+}
+		
+
 =item B<as_graphml>
 
-print $graph->as_graphml( $recalculate )
+print $collation->as_graphml( $recalculate )
 
 Returns a GraphML representation of the collation graph, with
 transposition information and position information. Unless
@@ -278,14 +472,13 @@ 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;
+    my( $self ) = @_;
 
     # 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';
+        'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
 
     # Create the document and root node
     my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
@@ -294,173 +487,264 @@ 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/ version 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', 'reading', '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 );
+    my %node_data_keys;
+    my $ndi = 0;
+    my %node_data = ( 
+    	id => 'string',
+    	text => 'string',
+    	rank => 'string',
+    	is_start => 'boolean',
+    	is_end => 'boolean',
+    	is_lacuna => 'boolean',
+    	);
+    foreach my $datum ( keys %node_data ) {
+        $node_data_keys{$datum} = 'dn'.$ndi++;
+        my $key = $root->addNewChild( $graphml_ns, 'key' );
+        $key->setAttribute( 'attr.name', $datum );
+        $key->setAttribute( 'attr.type', $node_data{$datum} );
+        $key->setAttribute( 'for', 'node' );
+        $key->setAttribute( 'id', $node_data_keys{$datum} );
     }
 
     # Add the data keys for edges, i.e. witnesses
-    my $wit_ctr = 0;
-    foreach my $wit_key( qw/ main ante_corr / ) {
-	my $key = $root->addNewChild( $graphml_ns, 'key' );
-	$key->setAttribute( 'attr.name', "witness_$wit_key" );
-	$key->setAttribute( 'attr.type', 'string' );
-	$key->setAttribute( 'for', 'edge' );
-	$key->setAttribute( 'id', 'w'.$wit_ctr++ );
+    my $edi = 0;
+    my %edge_data_keys;
+    my %edge_data = (
+    	class => 'string',				# Class, deprecated soon
+    	witness => 'string',			# ID/label for a path
+    	relationship => 'string',		# ID/label for a relationship
+    	extra => 'boolean',				# Path key
+    	colocated => 'boolean',			# Relationship key
+    	non_correctable => 'boolean',	# Relationship key
+    	non_independent => 'boolean',	# Relationship key
+    	);
+    foreach my $datum ( keys %edge_data ) {
+        $edge_data_keys{$datum} = 'de'.$edi++;
+        my $key = $root->addNewChild( $graphml_ns, 'key' );
+        $key->setAttribute( 'attr.name', $datum );
+        $key->setAttribute( 'attr.type', $edge_data{$datum} );
+        $key->setAttribute( 'for', 'edge' );
+        $key->setAttribute( 'id', $edge_data_keys{$datum} );
     }
 
-    # 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' );
+    # Add the collation graph itself
+    my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
+    $sgraph->setAttribute( 'edgedefault', 'directed' );
+    $sgraph->setAttribute( 'id', $self->tradition->name );
+    $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
+    $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
+    $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
+    $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
+    $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
+    	    
+    # Collation attribute data
+    foreach my $datum ( @graph_attributes ) {
+    	my $value = $datum eq 'version' ? '3.0' : $self->$datum;
+		_add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
+	}
 
     my $node_ctr = 0;
     my %node_hash;
-    foreach my $n ( sort { $a->name cmp $b->name } $self->readings ) {
-	my %this_node_data = ();
-	foreach my $ndi ( 0 .. $#node_data ) {
-	    my $key = $node_data[$ndi];
-	    if( $key eq 'name' ) {
-		$this_node_data{'d'.$ndi} = $n->name;
-	    } elsif( $key eq 'token' ) {
-		$this_node_data{'d'.$ndi} = $n->label;
-	    } elsif( $key eq 'identical' && $n->has_primary ) {
-		$this_node_data{'d'.$ndi} = $n->primary->name;
-	    } elsif( $key eq 'position' ) {
-		$this_node_data{'d'.$ndi} = $n->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->appendText( $this_node_data{$dk} );
-	}
+    # Add our readings to the graph
+    foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
+    	# Add to the main graph
+        my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
+        my $node_xmlid = 'n' . $node_ctr++;
+        $node_hash{ $n->id } = $node_xmlid;
+        $node_el->setAttribute( 'id', $node_xmlid );
+        foreach my $d ( keys %node_data ) {
+        	my $nval = $n->$d;
+        	_add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
+        		if defined $nval;
+        }
     }
 
+    # Add the path edges to the sequence graph
     my $edge_ctr = 0;
-    foreach my $e ( sort { $a->from->name cmp $b->from->name } $self->paths() ) {
-	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 witness
-	my $base = $e->label;
-	my $key = 'w0';
-	# TODO kind of hacky
-	if( $e->label =~ /^(.*?)\s+(\(a\.c\.\))$/ ) {
-	    $base = $1;
-	    $key = 'w1';
+    foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
+    	# We add an edge in the graphml for every witness in $e.
+    	foreach my $wit ( $self->path_witnesses( $e ) ) {
+			my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
+										$node_hash{ $e->[0] },
+										$node_hash{ $e->[1] } );
+			my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
+			$edge_el->setAttribute( 'source', $from );
+			$edge_el->setAttribute( 'target', $to );
+			$edge_el->setAttribute( 'id', $id );
+			
+			# It's a witness path, so add the witness
+			my $base = $wit;
+			my $key = $edge_data_keys{'witness'};
+			# Is this an ante-corr witness?
+			my $aclabel = $self->ac_label;
+			if( $wit =~ /^(.*)\Q$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'}, $aclabel );
+			}
+			_add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
+			_add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
+		}
 	}
-	my $wit_el = $edge_el->addNewChild( $graphml_ns, 'data' );
-	$wit_el->setAttribute( 'key', $key );
-	$wit_el->appendText( $base );
-    }
+	
+	# Add the relationship graph to the XML
+	$self->relations->as_graphml( $root );
 
-    # Return the thing
-    $self->_save_graphml( $graphml->toString(1) );
-    return $graphml->toString(1);
+    # Save and return the thing
+    my $result = decode_utf8( $graphml->toString(1) );
+    return $result;
 }
 
-sub _make_xml_attr {
-    my $str = shift;
-    $str =~ s/\s/_/g;
-    $str =~ s/\W//g;
-    $str =~ "a$str" if $str =~ /^\d/;
-    return $str;
+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 );
 }
 
-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 );
-	}
+=item B<as_csv>
 
-	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 );
-	    }
-	}
+print $collation->as_csv( $recalculate )
+
+Returns a CSV alignment table representation of the collation graph, one
+row per witness (or witness uncorrected.) 
+
+=cut
+
+sub as_csv {
+    my( $self ) = @_;
+    my $table = $self->make_alignment_table;
+    my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );    
+    my @result;
+    # Make the header row
+    $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
+	push( @result, decode_utf8( $csv->string ) );
+    # Make the rest of the rows
+    foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
+    	my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
+    	my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
+        $csv->combine( @row );
+        push( @result, decode_utf8( $csv->string ) );
     }
+    return join( "\n", @result );
+}
+
+=item B<make_alignment_table>
+
+my $table = $collation->make_alignment_table( $use_refs, \@wits_to_include )
+
+Return a reference to an alignment table, in a slightly enhanced CollateX
+format which looks like this:
 
-    $self->collapsed( 1 );
+ $table = { alignment => [ { witness => "SIGIL", 
+                             tokens => [ { t => "READINGTEXT" }, ... ] },
+                           { witness => "SIG2", 
+                             tokens => [ { t => "READINGTEXT" }, ... ] },
+                           ... ],
+            length => TEXTLEN };
+
+If $use_refs is set to 1, the reading object is returned in the table 
+instead of READINGTEXT; if not, the text of the reading is returned.
+If $wits_to_include is set to a hashref, only the witnesses whose sigil
+keys have a true hash value will be included.
+
+=cut
+
+sub make_alignment_table {
+    my( $self, $noderefs, $include ) = @_;
+    unless( $self->linear ) {
+        warn "Need a linear graph in order to make an alignment table";
+        return;
+    }
+    my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
+    my @all_pos = ( 1 .. $self->end->rank - 1 );
+    foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
+    	if( $include ) {
+    		next unless $include->{$wit->sigil};
+    	}
+        # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
+        my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
+        my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
+        push( @{$table->{'alignment'}}, 
+        	{ 'witness' => $wit->sigil, 'tokens' => \@row } );
+        if( $wit->is_layered ) {
+        	my @wit_ac_path = $self->reading_sequence( $self->start, $self->end, 
+        		$wit->sigil.$self->ac_label, $wit->sigil );
+            my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
+			push( @{$table->{'alignment'}},
+				{ 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
+        }           
+    }
+	return $table;
 }
 
-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, $_ );
-	}
+sub _make_witness_row {
+    my( $path, $positions, $noderefs ) = @_;
+    my %char_hash;
+    map { $char_hash{$_} = undef } @$positions;
+    my $debug = 0;
+    foreach my $rdg ( @$path ) {
+        my $rtext = $rdg->text;
+        $rtext = '#LACUNA#' if $rdg->is_lacuna;
+        print STDERR "rank " . $rdg->rank . "\n" if $debug;
+        # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
+        $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg } 
+        								   : { 't' => $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 : { 't' => '#LACUNA#' };
+        }
+        push( @filled_row, $el );
+        $last_el = $el;
     }
-    $self->collapsed( 0 );
+    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->{'t'} eq '#LACUNA#';
+    return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
+        && $el->{'t'}->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;        
 }
 
 =back
@@ -475,22 +759,16 @@ my $beginning = $collation->start();
 
 Returns the beginning of the collation, a meta-reading with label '#START#'.
 
-=cut
+=item B<end>
+
+my $end = $collation->end();
+
+Returns the end of the collation, a meta-reading with label '#END#'.
 
-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] );
+my @readings = $collation->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,
@@ -498,6 +776,8 @@ 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 ) = @_;
 
@@ -505,31 +785,33 @@ sub reading_sequence {
     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;
+    while( $n && $n->id ne $end->id ) {
+        if( exists( $seen{$n->id} ) ) {
+            warn "Detected loop at " . $n->id;
+            last;
+        }
+        $seen{$n->id} = 1;
+        
+        my $next = $self->next_reading( $n, $witness, $backup );
+        unless( $next ) {
+            warn "Did not find any path for $witness from reading " . $n->id;
+            last;
+        }
+        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;
+    warn "Last reading found from " . $start->text .
+        " for witness $witness is not the end!"
+        unless $last->id eq $end->id;
     
     return @readings;
 }
 
 =item B<next_reading>
 
-my $next_reading = $graph->next_reading( $reading, $witpath );
+my $next_reading = $collation->next_reading( $reading, $witpath );
 
 Returns the reading that follows the given reading along the given witness
 path.  
@@ -539,12 +821,14 @@ path.
 sub next_reading {
     # Return the successor via the corresponding path.
     my $self = shift;
-    return $self->_find_linked_reading( 'next', @_ );
+    my $answer = $self->_find_linked_reading( 'next', @_ );
+	return undef unless $answer;
+    return $self->reading( $answer );
 }
 
 =item B<prior_reading>
 
-my $prior_reading = $graph->prior_reading( $reading, $witpath );
+my $prior_reading = $collation->prior_reading( $reading, $witpath );
 
 Returns the reading that precedes the given reading along the given witness
 path.  
@@ -554,46 +838,47 @@ path.
 sub prior_reading {
     # Return the predecessor via the corresponding path.
     my $self = shift;
-    return $self->_find_linked_reading( 'prior', @_ );
+    my $answer = $self->_find_linked_reading( 'prior', @_ );
+    return $self->reading( $answer );
 }
 
 sub _find_linked_reading {
     my( $self, $direction, $node, $path, $alt_path ) = @_;
     my @linked_paths = $direction eq 'next' 
-	? $node->outgoing() : $node->incoming();
+        ? $self->sequence->edges_from( $node ) 
+        : $self->sequence->edges_to( $node );
     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;
+    @path_wits = sort( $self->witnesses_of_label( $path ) ) if $path;
+    @alt_path_wits = sort( $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;
-	    }
-	}
+        if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
+            $base_le = $le;
+        }
+		my @le_wits = $self->path_witnesses( $le );
+		if( _is_within( \@path_wits, \@le_wits ) ) {
+			# This is the right path.
+			return $direction eq 'next' ? $le->[1] : $le->[0];
+		} 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;
+    return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
+        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;
+    return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
+        if $base_le;
 
     # Got this far? We have no appropriate path.
-    warn "Could not find $direction node from " . $node->label 
-	. " along path $path";
+    warn "Could not find $direction node from " . $node->id 
+        . " along path $path";
     return undef;
 }
 
@@ -602,88 +887,26 @@ 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;
+        $ret = 0 unless grep { /^\Q$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.
+# 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.
+# When we are done, clear out the witness path attributes, as they are no
+# longer needed.
+# TODO Find a way to replace the witness path attributes with encapsulated functions?
 
 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 );
+    foreach my $wit ( $self->tradition->witnesses ) {
+        # print STDERR "Making path for " . $wit->sigil . "\n";
+        $self->make_witness_path( $wit );
     }
-    return @common_readings;
 }
 
 sub make_witness_path {
@@ -691,307 +914,212 @@ sub make_witness_path {
     my @chain = @{$wit->path};
     my $sig = $wit->sigil;
     foreach my $idx ( 0 .. $#chain-1 ) {
-	$self->add_path( $chain[$idx], $chain[$idx+1], $sig );
+        $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 (a.c.)" )
-	    unless $self->has_path( $source, $target, $sig );
+    if( $wit->is_layered ) {
+        @chain = @{$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 );
+        }
     }
+    $wit->clear_path;
+    $wit->clear_uncorrected_path;
 }
 
-sub common_readings {
+sub calculate_ranks {
     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 );
+    # 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->id};
+        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 ) {
+                $rel_containers{$_->id} = $rn;
+            }
+        } else {
+            # Add a new node to mirror the old node.
+            $rel_containers{$r->id} = $r->id;
+            $topo_graph->add_vertex( $r->id );
+        }
     }
 
-    $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 );
+    # Add the edges.
+    foreach my $r ( $self->readings ) {
+        foreach my $n ( $self->sequence->successors( $r->id ) ) {
+        	my( $tfrom, $tto ) = ( $rel_containers{$r->id},
+        		$rel_containers{$n} );
+        	$DB::single = 1 unless $tfrom && $tto;
+            $topo_graph->add_edge( $tfrom, $tto );
+        }
     }
-    push( @$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.
-	}
+    # Now do the rankings, starting with the start node.
+    my $topo_start = $rel_containers{$self->start->id};
+    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 );
     }
-}
-
-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;
+    # Transfer our rankings from the topological graph to the real one.
+    foreach my $r ( $self->readings ) {
+        if( defined $node_ranks->{$rel_containers{$r->id}} ) {
+            $r->rank( $node_ranks->{$rel_containers{$r->id}} );
+        } else {
+            $DB::single = 1;
+            die "No rank calculated for node " . $r->id 
+                . " - do you have a cycle in the graph?";
+        }
     }
-    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;
+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;
 }
 
-## Lemmatizer functions
-
-sub init_lemmata {
+# 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;
-    
-    foreach my $position ( $self->all_positions ) {
-	$self->lemmata->{$position} = undef;
-    }
-
-    foreach my $cr ( $self->common_readings ) {
-	$self->lemmata->{$cr->position} = $cr->name;
+    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;
+        }
     }
 }
-    
-=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 * 
+## Utility functions
+    
+# Return the string that joins together a list of witnesses for
+# display on a single path.
+sub witnesses_of_label {
+    my( $self, $label ) = @_;
+    my $regex = $self->wit_list_separator;
+    my @answer = split( /\Q$regex\E/, $label );
+    return @answer;
+}    
 
-A state of 1 means 'lemmatize this reading'
+=begin testing
 
-=item * 
+use Text::Tradition;
 
-A state of 0 means 'delemmatize this reading'
+my $cxfile = 't/data/Collatex-16.xml';
+my $t = Text::Tradition->new( 
+    'name'  => 'inline', 
+    'input' => 'CollateX',
+    'file'  => $cxfile,
+    );
+my $c = $t->collation;
 
-=item * 
+is( $c->common_predecessor( $c->reading('n9'), $c->reading('n23') )->id, 
+    'n20', "Found correct common predecessor" );
+is( $c->common_successor( $c->reading('n9'), $c->reading('n23') )->id, 
+    '#END#', "Found correct common successor" );
 
-A state of undef means 'an ellipsis belongs in the text here because
-no decision has been made / an earlier decision was backed out'
+is( $c->common_predecessor( $c->reading('n19'), $c->reading('n17') )->id, 
+    'n16', "Found correct common predecessor for readings on same path" );
+is( $c->common_successor( $c->reading('n21'), $c->reading('n26') )->id, 
+    '#END#', "Found correct common successor for readings on same path" );
 
-=back
+=end testing
 
 =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;
+## Return the closest reading that is a predecessor of both the given readings.
+sub common_predecessor {
+	my $self = shift;
+	return $self->common_in_path( @_, 'predecessors' );
 }
 
-=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 common_successor {
+	my $self = shift;
+	return $self->common_in_path( @_, 'successors' );
 }
 
-sub same_position_as {
-    my( $self, $reading ) = @_;
-    my $pos = $reading->position;
-    my @same = grep { $_ ne $reading } $self->readings_at_position( $reading->position );
-    return @same;
+sub common_in_path {
+	my( $self, $r1, $r2, $dir ) = @_;
+	my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
+	$iter = $self->end->rank - $iter if $dir eq 'successors';
+	my @candidates;
+	my @last_checked = ( $r1, $r2 );
+	my %all_seen;
+	while( !@candidates ) {
+		my @new_lc;
+		foreach my $lc ( @last_checked ) {
+			foreach my $p ( $lc->$dir ) {
+				if( $all_seen{$p->id} ) {
+					push( @candidates, $p );
+				} else {
+					$all_seen{$p->id} = 1;
+					push( @new_lc, $p );
+				}
+			}
+		}
+		@last_checked = @new_lc;
+	}
+	my @answer = sort { $a->rank <=> $b->rank } @candidates;
+	return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
 }
 
-# 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, @_ );
-}
+no Moose;
+__PACKAGE__->meta->make_immutable;
 
-sub witnesses_of_label {
-    my( $self, $label ) = @_;
-    my $regex = $self->wit_list_separator;
-    my @answer = split( /\Q$regex\E/, $label );
-    return @answer;
-}    
+=head1 BUGS / TODO
 
-sub unique_list {
-    my( @list ) = @_;
-    my %h;
-    map { $h{$_->name} = $_ } @list;
-    return values( %h );
-}
+=over
 
-sub add_hash_entry {
-    my( $hash, $key, $entry ) = @_;
-    if( exists $hash->{$key} ) {
-	push( @{$hash->{$key}}, $entry );
-    } else {
-	$hash->{$key} = [ $entry ];
-    }
-}
+=item * Think about making Relationship objects again
 
-no Moose;
-__PACKAGE__->meta->make_immutable;
+=back