make Analysis work with the new alignment table

[scpubgit/stemmatology.git] / lib / Text / Tradition / Collation.pm

package Text::Tradition::Collation;

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 XML::LibXML;
use Moose;

has 'sequence' => (
    is => 'ro',
    isa => 'Graph',
    default => sub { Graph->new() },
    handles => {
    	paths => 'edges',
    },
    );
    
has 'relations' => (
	is => 'ro',
	isa => 'Graph',
	default => sub { Graph->new( undirected => 1 ) },
    handles => {
    	relationships => 'edges',
    },
	);

has 'tradition' => (
    is => 'ro',
    isa => 'Text::Tradition',
    weak_ref => 1,
    );

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',
    isa => 'Str',
    default => ', ',
    );

has 'baselabel' => (
    is => 'rw',
    isa => 'Str',
    default => 'base text',
    );

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
#    the results as in 2.
# 2. Read a pre-prepared collation in one of a variety of formats,
#    and make the graph from that.

# The graph itself will (for now) be immutable, and the positions
# within the graph will also be immutable.  We need to calculate those
# positions upon graph construction.  The equivalences between graph
# nodes will be mutable, entirely determined by the user (or possibly
# by some semantic pre-processing provided by the user.)  So the
# constructor should just make an empty equivalences object.  The
# constructor will also need to make the witness objects, if we didn't
# come through option 1.

sub BUILD {
    my $self = shift;
    $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
    $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
}

### Reading construct/destruct functions

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_vertex( $reading->id );
	return $reading;
};

around del_reading => sub {
	my $orig = shift;
	my $self = shift;
	my $arg = shift;
	
	if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
		$arg = $arg->id;
	}
	# Remove the reading from the graphs.
	$self->sequence->delete_vertex( $arg );
	$self->relations->delete_vertex( $arg );
	
	# Carry on.
	$self->$orig( $arg );
};

# merge_readings( $main, $to_be_deleted );

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 );
	}
	foreach my $rel ( $self->relations->edges_at( $deleted ) ) {
		my @vector = ( $kept );
		push( @vector, $rel->[0] eq $deleted ? $rel->[1] : $rel->[0] );
		next if $vector[0] eq $vector[1]; # Don't add a self loop
		# Is there a relationship here already? If so, keep it.
		# TODO Warn about conflicting relationships
		next if $self->relations->has_edge( @vector );
		# If not, adopt the relationship that would be deleted.
		$self->relations->add_edge( @vector );
		my $attr = $self->relations->get_edge_attributes( @$rel );
		$self->relations->set_edge_attributes( @vector, $attr );
	}
	
	# 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 );
}


# 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 );
};

sub del_path {
	my $self = shift;
	my @args;
	if( ref( $_[0] ) eq 'ARRAY' ) {
		my $e = shift @_;
		@args = ( @$e, @_ );
	} else {
		@args = @_;
	}

	# 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 = 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 );
}

### Relationship logic

=head2 add_relationship( $reading1, $reading2, $definition )

Adds the specified relationship between the two readings.  A relationship
is transitive (i.e. undirected), and must have the following attributes
specified in the hashref $definition:

=over 4

=item * type - Can be one of spelling, orthographic, grammatical, meaning, lexical, collated, repetition, transposition.  All but the last two are only valid relationships between readings that occur at the same point in the text.

=item * non_correctable - (Optional) True if the reading would not have been corrected independently.

=item * non_independent - (Optional) True if the variant is unlikely to have occurred independently in unrelated witnesses.

=item * global - (Optional) A meta-attribute, to set the same relationship between readings with the same text whenever they occur in the same place.

=back

=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 = shift;
    my( $source, $target, $options ) = $self->_stringify_args( @_ );

	# Check the options
	if( !defined $options->{'type'} ||
		$options->{'type'} !~ /^(spelling|orthographic|grammatical|meaning|lexical|collated|repetition|transposition)$/i ) {
		my $t = $options->{'type'} ? $options->{'type'} : '';
		return( undef, "Invalid or missing type " . $options->{'type'} );
	}
	unless ( $options->{'type'} =~ /^(repetition|transposition)$/ ) {
		$options->{'colocated'} = 1;
	}
	
    # Make sure there is not another relationship between these two
    # readings already
    if( $self->relations->has_edge( $source, $target ) ) {
		return ( undef, "Relationship already exists between these readings" );
    }
    if( !$self->relationship_valid( $source, $target, $options->{'type'} ) ) {
        return ( undef, 'Relationship creates witness loop' );
    }

	my @vector = ( $source, $target );
	$self->relations->add_edge( @vector );
	$self->relations->set_edge_attributes( @vector, $options );
    
    # TODO Handle global relationship setting

    return( 1, @vector );
}

sub relationship_valid {
    my( $self, $source, $target, $rel ) = @_;
    if( $rel eq 'repetition' ) {
    	return 1;
	} elsif ( $rel eq 'transposition' ) {
		# Check that the two readings do not appear in the same witness.
		my %seen_wits;
		map { $seen_wits{$_} = 1 } $self->reading_witnesses( $source );
		foreach my $w ( $self->reading_witnesses( $target ) ) {
			return 0 if $seen_wits{$w};
		}
		return 1;
	} else {
		# Check that linking the source and target in a relationship won't lead
		# to a path loop for any witness.  First make a lookup table of all the
		# readings related to either the source or the target.
		my @proposed_related = ( $source, $target );
		push( @proposed_related, $self->related_readings( $source, 'colocated' ) );
		push( @proposed_related, $self->related_readings( $target, 'colocated' ) );
		my %pr_ids;
		map { $pr_ids{ $_ } = 1 } @proposed_related;
	
		# None of these proposed related readings should have a neighbor that
		# is also in proposed_related.
		foreach my $pr ( keys %pr_ids ) {
			foreach my $neighbor( $self->sequence->neighbors( $pr ) ) {
				return 0 if exists $pr_ids{$neighbor};
			}
		}		
		return 1;
	}
}

# Return a list of the witnesses in which the reading appears.
sub reading_witnesses {
	my( $self, $reading ) = @_;
	# We need only check either the incoming or the outgoing edges; I have
	# arbitrarily chosen "incoming".
	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;
}

sub related_readings {
	my( $self, $reading, $colocated ) = @_;
	my $return_object;
	if( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
		$reading = $reading->id;
		$return_object = 1;
# 		print STDERR "Returning related objects\n";
# 	} else {
# 		print STDERR "Returning related object names\n";
	}
	my @related = $self->relations->all_reachable( $reading );
	if( $colocated ) {
		my @colo = grep { $self->relations->has_edge_attribute( $reading, $_, 'colocated' ) } @related;
		@related = @colo;
	} 
	return $return_object ? map { $self->reading( $_ ) } @related : @related;
}

=head2 Output method(s)

=over

=item B<as_svg>

print $graph->as_svg( $recalculate );

Returns an SVG string that represents the graph, via as_dot and graphviz.

=cut

sub as_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<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 = 'sequence' unless $view;
    # TODO consider making some of these things configurable
    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 .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
                     11, "white", "filled", "ellipse" );

    foreach my $reading ( $self->readings ) {
        # 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 );
    }
    
    # TODO do something sensible for relationships

    my @edges = $self->paths;
    foreach my $edge ( @edges ) {
        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 )

Returns a GraphML representation of the collation graph, with
transposition information and position information. Unless
$recalculate is passed (and is a true value), the method will return a
cached copy of the SVG after the first call to the method.

=cut

sub as_graphml {
    my( $self ) = @_;

    # Some namespaces
    my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
    my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
    my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
        'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';

    # Create the document and root node
    my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
    my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
    $graphml->setDocumentElement( $root );
    $root->setNamespace( $xsi_ns, 'xsi', 0 );
    $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );

    # Add the data keys for 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_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 $edi = 0;
    my %edge_data_keys;
    my %edge_data = (
    	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 collation graphs themselves
    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' );
    
    my $rgraph = $root->addNewChild( $graphml_ns, 'graph' );
    $rgraph->setAttribute( 'edgedefault', 'undirected' );
    $rgraph->setAttribute( 'id', 'relationships' );
    $rgraph->setAttribute( 'parse.edgeids', 'canonical' );
    $rgraph->setAttribute( 'parse.edges', scalar($self->relationships) );
    $rgraph->setAttribute( 'parse.nodeids', 'canonical' );
    $rgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
    $rgraph->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;
    # Add our readings to the graphs
    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 to the relationships graph
        my $rnode_el = $rgraph->addNewChild( $graphml_ns, 'node' );
        $rnode_el->setAttribute( 'id', $node_xmlid );
    }

    # Add the path edges to the sequence graph
    my $edge_ctr = 0;
    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 the relationship edges to the relationships graph
	foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->relationships ) {
		my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
									$node_hash{ $e->[0] },
									$node_hash{ $e->[1] } );
		my $edge_el = $rgraph->addNewChild( $graphml_ns, 'edge' );
		$edge_el->setAttribute( 'source', $from );
		$edge_el->setAttribute( 'target', $to );
		$edge_el->setAttribute( 'id', $id );
		
		my $data = $self->relations->get_edge_attributes( @$e );
		# It's a relationship, so save the relationship data
		_add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $data->{type} );
		_add_graphml_data( $edge_el, $edge_data_keys{'colocated'}, $data->{colocated} );
		if( exists $data->{non_correctable} ) {
			_add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'}, 
				$data->{non_correctable} );
		}
		if( exists $data->{non_independent} ) {
			_add_graphml_data( $edge_el, $edge_data_keys{'non_independent'}, 
				$data->{non_independent} );
		}
    }

    # Save and return the thing
    my $result = decode_utf8( $graphml->toString(1) );
    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.) 

=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 { $_->[$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 = $graph->make_alignment_table( $use_refs, \@wits_to_include )

Return a reference to an alignment table, in the format described at
L<http://gregor.middell.net/collatex>.  If $use_refs is set to 1, the reading
object is returned in the table; if not, the text of the reading is returned.
If $wits_to_include is set to an arrayref, only the witnesses listed will be 
included in the table.

=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 ( $self->tradition->witnesses ) {
    	if( $include ) {
    		next unless grep { $_ eq $wit->sigil } @$include;
    	}
    	$DB::single = 1 if $wit->sigil eq 'U';
        # 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 _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 ? { 't' => $last_el } : { 't' => '#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->{'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

=head2 Navigation methods

=over

=item B<start>

my $beginning = $collation->start();

Returns the beginning of the collation, a meta-reading with label '#START#'.

=item B<end>

my $end = $collation->end();

Returns the end of the collation, a meta-reading with label '#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->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->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 );

Returns the reading that follows the given reading along the given witness
path.  

=cut

sub next_reading {
    # Return the successor via the corresponding path.
    my $self = shift;
    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 );

Returns the reading that precedes the given reading along the given witness
path.  

=cut

sub prior_reading {
    # Return the predecessor via the corresponding path.
    my $self = shift;
    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' 
        ? $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 = 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( $self->sequence->has_edge_attribute( @$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->[1] : $alt_le->[0]
        if $alt_le;

    # Got this far? Return the base path if it exists.
    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->id 
        . " along path $path";
    return undef;
}

# Some set logic.
sub _is_within {
    my( $set1, $set2 ) = @_;
    my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
    foreach my $el ( @$set1 ) {
        $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
    }
    return $ret;
}


## INITIALIZATION METHODS - for use by parsers

# 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 ) = @_;
    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( $wit->is_layered ) {
        @chain = @{$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 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->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 );
        }
    }

    # 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 );
        }
    }
    
    # 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 );
    }
    # 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?";
        }
    }
}

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;
        }
    }
}


## 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;
}    

no Moose;
__PACKAGE__->meta->make_immutable;

=head1 BUGS / TODO

=over

=item * Think about making Relationship objects again

=back