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

package Text::Tradition::Collation;

use Graph::Easy;
use IPC::Run qw( run binary );
use Text::Tradition::Collation::Reading;
use Moose;

has 'graph' => (
    is => 'ro',
    isa => 'Graph::Easy',
    handles => {
	add_reading => 'add_node',
	del_reading => 'del_node',
	add_path => 'add_edge',
	del_path => 'del_edge',
	reading => 'node',
	path => 'edge',
	readings => 'nodes',
	paths => 'edges',
    },
    default => sub { Graph::Easy->new( undirected => 0 ) },
    );
		

has 'tradition' => (
    is => 'rw',
    isa => 'Text::Tradition',
    );

has 'svg' => (
    is => 'ro',
    isa => 'Str',
    writer => '_save_svg',
    predicate => 'has_svg',
    );

has 'graphviz' => (
    is => 'ro',
    isa => 'Str',
    writer => '_save_graphviz',
    predicate => 'has_graphviz',
    );

has 'graphml' => (
    is => 'ro',
    isa => 'XML::LibXML::Document',
    writer => '_save_graphml',
    predicate => 'has_graphml',
    );

# Keeps track of the lemmas within the collation.  At most one lemma
# per position in the graph.
has 'lemmata' => (
    is => 'ro',
    isa => 'HashRef[Maybe[Str]]',
    default => sub { {} },
    );

has 'wit_list_separator' => (
			     is => 'rw',
			     isa => 'Str',
			     default => ', ',
			     );

# 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, $args ) = @_;
    $self->graph->use_class('node', 'Text::Tradition::Collation::Reading');

    # Pass through any graph-specific options.
    my $shape = exists( $args->{'shape'} ) ? $args->{'shape'} : 'ellipse';
    $self->graph->set_attribute( 'node', 'shape', $shape );
}

# Wrappes around merge_nodes

sub merge_readings {
    my $self = shift;
    my $first_node = shift;
    my $second_node = shift;
    $first_node->merge_from( $second_node );
    unshift( @_, $first_node, $second_node );
    return $self->graph->merge_nodes( @_ );
}

=head2 Output method(s)

=over

=item B<as_svg>

print $graph->as_svg( $recalculate );

Returns an SVG string that represents the graph.  Uses GraphViz to do
this, because Graph::Easy doesn\'t cope well with long graphs. Unless
$recalculate is passed (and is a true value), the method will return a
cached copy of the SVG after the first call to the method.

=cut

sub as_svg {
    my( $self, $recalc ) = @_;
    return $self->svg if $self->has_svg;
    
    $self->_save_graphviz( $self->graph->as_graphviz() )
	unless( $self->has_graphviz && !$recalc );
    
    my @cmd = qw/dot -Tsvg/;
    my( $svg, $err );
    my $in = $self->graphviz;
    run( \@cmd, \$in, ">", binary(), \$svg );
    $self->{'svg'} = $svg;
    return $svg;
}

=item B<as_graphml>

print $graph->as_graphml( $recalculate )

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

=cut

sub as_graphml {
    my( $self, $recalc ) = @_;
    return $self->graphml if $self->has_graphml;

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

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

    # Add the data keys for nodes
    my @node_data = ( 'name', 'token', 'identical', 'position' );
    foreach my $ndi ( 0 .. $#node_data ) {
	my $key = $root->addNewChild( $graphml_ns, 'key' );
	$key->setAttribute( 'attr.name', $node_data[$ndi] );
	$key->setAttribute( 'attr.type', 'string' );
	$key->setAttribute( 'for', 'node' );
	$key->setAttribute( 'id', 'd'.$ndi );
    }

    # Add the data keys for edges
    my %wit_hash;
    my $wit_ctr = 0;
    foreach my $wit ( $self->getWitnessList ) {
	my $wit_key = 'w' . $wit_ctr++;
	$wit_hash{$wit} = $wit_key;
	my $key = $root->addNewChild( $graphml_ns, 'key' );
	$key->setAttribute( 'attr.name', $wit );
	$key->setAttribute( 'attr.type', 'string' );
	$key->setAttribute( 'for', 'edge' );
	$key->setAttribute( 'id', $wit_key );
    }

    # 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', $self->edges() );
    $graph->setAttribute( 'parse.nodeids', 'canonical' );
    $graph->setAttribute( 'parse.nodes', $self->nodes() );
    $graph->setAttribute( 'parse.order', 'nodesfirst' );

    my $node_ctr = 0;
    my %node_hash;
    foreach my $n ( $self->readings ) {
	my %this_node_data = ();
	foreach my $ndi ( 0 .. $#node_data ) {
	    my $value;
	    $this_node_data{'d'.$ndi} = $n->name if $node_data[$ndi] eq 'name';
	    $this_node_data{'d'.$ndi} = $n->label 
		if $node_data[$ndi] eq 'token';
	    $this_node_data{'d'.$ndi} = $n->primary->name if $n->has_primary;
	    $this_node_data{'d'.$ndi} = 
		$self->{'positions'}->node_position( $n )
		if $node_data[$ndi] eq 'position';
	}
	my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
	my $node_xmlid = 'n' . $node_ctr++;
	$node_hash{ $n->name } = $node_xmlid;
	$node_el->setAttribute( 'id', $node_xmlid );
	    
	foreach my $dk ( keys %this_node_data ) {
	    my $d_el = $node_el->addNewChild( $graphml_ns, 'data' );
	    $d_el->setAttribute( 'key', $dk );
	    $d_el->appendTextChild( $this_node_data{$dk} );
	}
    }

    foreach my $e ( $self->edges() ) {
	my( $name, $from, $to ) = ( $e->name,
				    $node_hash{ $e->from()->name() },
				    $node_hash{ $e->to()->name() } );
	my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
	$edge_el->setAttribute( 'source', $from );
	$edge_el->setAttribute( 'target', $to );
	$edge_el->setAttribute( 'id', $name );
	# TODO Got to add the witnesses
    }

    # Return the thing
    $self->_save_graphml( $graphml );
    return $graphml;
}

=back

=head2 Navigation methods

=over

=item B<start>

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

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

=cut

sub start {
    # Return the beginning reading of the graph.
    my $self = shift;
    my( $new_start ) = @_;
    if( $new_start ) {
	$self->del_reading( '#START#' );
	$self->graph->rename_node( $new_start, '#START#' );
    }
    return $self->reading('#START#');
}

=item B<next_reading>

my $next_reading = $graph->next_reading( $reading, $witpath );

Returns the reading that follows the given reading along the given witness
path.  TODO These are badly named.

=cut

sub next_reading {
    # Return the successor via the corresponding edge.
    my $self = shift;
    return $self->_find_linked_reading( 'next', @_ );
}

=item B<prior_reading>

my $prior_reading = $graph->prior_reading( $reading, $witpath );

Returns the reading that precedes the given reading along the given witness
path.  TODO These are badly named.

=cut

sub prior_reading {
    # Return the predecessor via the corresponding edge.
    my $self = shift;
    return $self->_find_linked_reading( 'prior', @_ );
}

sub _find_linked_reading {
    my( $self, $direction, $node, $edge ) = @_;
    $edge = 'base text' unless $edge;
    my @linked_edges = $direction eq 'next' 
	? $node->outgoing() : $node->incoming();
    return undef unless scalar( @linked_edges );
    
    # We have to find the linked edge that contains all of the
    # witnesses supplied in $edge.
    my @edge_wits = $self->witnesses_of_label( $edge );
    foreach my $le ( @linked_edges ) {
	my @le_wits = $self->witnesses_of_label( $le->name );
	if( _is_within( \@edge_wits, \@le_wits ) ) {
	    # This is the right edge.
	    return $direction eq 'next' ? $le->to() : $le->from();
	}
    }
    warn "Could not find $direction node from " . $node->label 
	. " along edge $edge";
    return undef;
}

# Some set logic.
sub _is_within {
    my( $set1, $set2 ) = @_;
    my $ret = 1;
    foreach my $el ( @$set1 ) {
	$ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
    }
    return $ret;
}


## INITIALIZATION METHODS - for use by parsers
# Walk the paths for each witness in the graph, and return the nodes
# that the graph has in common.

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 = ( $curr_reading );
	my %seen_readings;
	# TODO Detect loops at some point
	while( $curr_reading->name ne $end->name ) {
	    if( $seen_readings{$curr_reading->name} ) {
		warn "Detected loop walking path for witness " . $wit->sigil
		    . " at reading " . $curr_reading->name;
		last;
	    }
	    my $next_reading = $self->next_reading( $curr_reading, 
						    $wit->sigil );
	    push( @wit_path, $next_reading );
	    $seen_readings{$curr_reading->name} = 1;
	    $curr_reading = $next_reading;
	}
	$wit->path( \@wit_path );
	if( @common_readings ) {
	    my @cn;
	    foreach my $n ( @wit_path ) {
		push( @cn, $n ) if grep { $_ eq $n } @common_readings;
	    }
	    @common_readings = ();
	    push( @common_readings, @cn );
	} else {
	    push( @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 common_readings {
    my $self = shift;
    my @common = grep { $_->is_common } $self->readings();
    return sort { _cmp_position( $a->position, $b->position ) } @common;
}

# Calculate the relative positions of nodes in the graph, if they
# were not given to us.
sub calculate_positions {
    my( $self, @ordered_common ) = @_;

    # We have to calculate the position identifiers for each word,
    # keyed on the common nodes.  This will be 'fun'.  The end result
    # is a hash per witness, whose key is the word node and whose
    # value is its position in the text.  Common nodes are always N,1
    # so have identical positions in each text.

    my $node_pos = {};
    foreach my $wit ( @{$self->tradition->witnesses} ) {
	# First we walk each path, making a matrix for each witness that
	# corresponds to its eventual position identifier.  Common nodes
	# always start a new row, and are thus always in the first column.

	my $wit_matrix = [];
	my $cn = 0;  # We should hit the common readings in order.
	my $row = [];
	foreach my $wn ( @{$wit->path} ) {
	    if( $wn eq $ordered_common[$cn] ) {
		# Set up to look for the next common node, and
		# start a new row of words.
		$cn++;
		push( @$wit_matrix, $row ) if scalar( @$row );
		$row = [];
	    }
	    push( @$row, $wn );
	}
	push( @$wit_matrix, $row );  # Push the last row onto the matrix

	# Now we have a matrix per witness, so that each row in the
	# matrix begins with a common node, and continues with all the
	# variant words that appear in the witness.  We turn this into
	# real positions in row,cell format.  But we need some
	# trickery in order to make sure that each node gets assigned
	# to only one position.

	foreach my $li ( 1..scalar(@$wit_matrix) ) {
	    foreach my $di ( 1..scalar(@{$wit_matrix->[$li-1]}) ) {
		my $reading = $wit_matrix->[$li-1]->[$di-1];
		my $position = "$li,$di";
		# If we have seen this node before, we need to compare
		# its position with what went before.
		unless( $reading->has_position &&
			_cmp_position( $position, $reading->position ) < 1 ) {
		    # The new position ID replaces the old one.
		    $reading->position( $position );
		} # otherwise, the old position needs to stay.
	    }
	}
    }

    $self->init_lemmata();
}

sub _cmp_position {
    my( $a, $b ) = @_;
    if ( $a && $b ) {
	my @pos_a = split(/,/, $a );
	my @pos_b = split(/,/, $b );

	my $big_cmp = $pos_a[0] <=> $pos_b[0];
	return $big_cmp if $big_cmp;
	# else 
	return $pos_a[1] <=> $pos_b[1];
    } elsif ( $b ) { # a is undefined
	return -1;
    } elsif ( $a ) { # b is undefined
	return 1;
    }
    return 0; # they are both undefined
}

sub all_positions {
    my $self = shift;
    my %positions = ();
    map { $positions{$_->position} = 1 } $self->readings;
    my @answer = sort { _cmp_position( $a, $b ) } keys( %positions );
    return @answer;
}

sub readings_at_position {
    my( $self, $pos ) = @_;
    my @answer = grep { $_->position eq $pos } $self->readings;
    return @answer;
}

## Lemmatizer functions

sub init_lemmata {
    my $self = shift;
    
    foreach my $position ( $self->all_positions ) {
	$self->lemmata->{$position} = undef;
    }

    foreach my $cr ( $self->common_readings ) {
	$self->lemmata->{$cr->position} = $cr->name;
    }
}
    
=item B<lemma_readings>

my @state = $graph->lemma_readings( @readings_delemmatized );

Takes a list of readings that have just been delemmatized, and returns
a set of tuples of the form ['reading', 'state'] that indicates what
changes need to be made to the graph.

=over

=item * 

A state of 1 means 'lemmatize this reading'

=item * 

A state of 0 means 'delemmatize this reading'

=item * 

A state of undef means 'an ellipsis belongs in the text here because
no decision has been made / an earlier decision was backed out'

=back

=cut

sub lemma_readings {
    my( $self, @toggled_off_nodes ) = @_;

    # First get the positions of those nodes which have been
    # toggled off.
    my $positions_off = {};
    map { $positions_off->{ $_->position } = $_->name } @toggled_off_nodes;

    # Now for each position, we have to see if a node is on, and we
    # have to see if a node has been turned off.
    my @answer;
    foreach my $pos ( $self->all_positions() ) {
	# Find the state of this position.  If there is an active node,
	# its name will be the state; otherwise the state will be 0 
	# (nothing at this position) or undef (ellipsis at this position)
	my $active = $self->lemmata->{$pos};
	
	# Is there a formerly active node that was toggled off?
	if( exists( $positions_off->{$pos} ) ) {
	    my $off_node = $positions_off->{$pos};
	    if( $active && $active ne $off_node) {
		push( @answer, [ $off_node, 0 ], [ $active, 1 ] );
	    } else {
		push( @answer, [ $off_node, $active ] );
	    }

	# No formerly active node, so we just see if there is a currently
	# active one.
	} elsif( $active ) {
	    # Push the active node, whatever it is.
	    push( @answer, [ $active, 1 ] );
	} else {
	    # Push the state that is there. Arbitrarily use the first node
	    # at that position.
	    my @pos_nodes = $self->readings_at_position( $pos );
	    push( @answer, [ $pos_nodes[0]->name, $self->lemmata->{$pos} ] );
	}
    }
    
    return @answer;
}

=item B<toggle_reading>

my @readings_delemmatized = $graph->toggle_reading( $reading_name );

Takes a reading node name, and either lemmatizes or de-lemmatizes
it. Returns a list of all readings that are de-lemmatized as a result
of the toggle.

=cut

sub toggle_reading {
    my( $self, $rname ) = @_;
    
    return unless $rname;
    my $reading = $self->reading( $rname );
    if( !$reading || $reading->is_common() ) {
	# Do nothing, it's a common node.
	return;
    } 
    
    my $pos = $reading->position;
    my $old_state = $self->lemmata->{$pos};
    my @readings_off;
    if( $old_state && $old_state eq $rname ) {
	# Turn off the node. We turn on no others by default.
	push( @readings_off, $reading );
    } else {
	# Turn on the node.
	$self->lemmata->{$pos} = $rname;
	# Any other 'on' readings in the same position should be off.
	push( @readings_off, $self->same_position_as( $reading ) );
	# Any node that is an identical transposed one should be off.
	push( @readings_off, $reading->identical_readings );
    }
    @readings_off = unique_list( @readings_off );

    # Turn off the readings that need to be turned off.
    my @readings_delemmatized;
    foreach my $n ( @readings_off ) {
	my $state = $self->lemmata->{$n->position};
	if( $state && $state eq $n->name ) { 
	    # this reading is still on, so turn it off
	    push( @readings_delemmatized, $n );
	    my $new_state = undef;
	    if( $n eq $reading ) {
		# This is the reading that was clicked, so if there are no
		# other readings there, turn off the position.  In all other
		# cases, restore the ellipsis.
		my @other_n = $self->same_position_as( $n );
		$new_state = 0 unless @other_n;
	    }
	    $self->lemmata->{$n->position} = $new_state;
	} elsif( $old_state && $old_state eq $n->name ) { 
	    # another reading has already been turned on here
	    push( @readings_delemmatized, $n );
	} # else some other reading was on anyway, so pass.
    }
    return @readings_delemmatized;
}

sub same_position_as {
    my( $self, $reading ) = @_;
    my $pos = $reading->position;
    my @same = grep { $_ ne $reading } $self->readings_at_position( $reading->position );
    return @same;
}

# Return the string that joins together a list of witnesses for
# display on a single path.
sub path_label {
    my $self = shift;
    return join( $self->wit_list_separator, @_ );
}

sub witnesses_of_label {
    my( $self, $label ) = @_;
    my $regex = $self->wit_list_separator;
    my @answer = split( /\Q$regex\E/, $label );
    return @answer;
}    

sub unique_list {
    my( @list ) = @_;
    my %h;
    map { $h{$_->name} = $_ } @list;
    return values( %h );
}

no Moose;
__PACKAGE__->meta->make_immutable;
Commit	Line	Data
dd3b58b0	1	package Text::Tradition::Collation;
d047cd52	2
d047cd52	3	use Graph::Easy;
8e1394aa	4	use IPC::Run qw( run binary );
8e1394aa	5	use Text::Tradition::Collation::Reading;
dd3b58b0	6	use Moose;
	7
	8	has 'graph' => (
d047cd52	9	is => 'ro',
	10	isa => 'Graph::Easy',
	11	handles => {
8e1394aa	12	add_reading => 'add_node',
	13	del_reading => 'del_node',
	14	add_path => 'add_edge',
	15	del_path => 'del_edge',
	16	reading => 'node',
	17	path => 'edge',
	18	readings => 'nodes',
	19	paths => 'edges',
d047cd52	20	},
	21	default => sub { Graph::Easy->new( undirected => 0 ) },
	22	);
784877d9	23
dd3b58b0	24
dd3b58b0	25	has 'tradition' => (
8e1394aa	26	is => 'rw',
d047cd52	27	isa => 'Text::Tradition',
d047cd52	28	);
dd3b58b0	29
8e1394aa	30	has 'svg' => (
	31	is => 'ro',
	32	isa => 'Str',
	33	writer => '_save_svg',
	34	predicate => 'has_svg',
	35	);
	36
	37	has 'graphviz' => (
	38	is => 'ro',
	39	isa => 'Str',
	40	writer => '_save_graphviz',
	41	predicate => 'has_graphviz',
	42	);
	43
	44	has 'graphml' => (
	45	is => 'ro',
	46	isa => 'XML::LibXML::Document',
	47	writer => '_save_graphml',
	48	predicate => 'has_graphml',
	49	);
	50
3a1f2523	51	# Keeps track of the lemmas within the collation. At most one lemma
	52	# per position in the graph.
	53	has 'lemmata' => (
	54	is => 'ro',
	55	isa => 'HashRef[Maybe[Str]]',
	56	default => sub { {} },
	57	);
	58
4a8828f0	59	has 'wit_list_separator' => (
	60	is => 'rw',
	61	isa => 'Str',
	62	default => ', ',
	63	);
	64
dd3b58b0	65	# The collation can be created two ways:
	66	# 1. Collate a set of witnesses (with CollateX I guess) and process
	67	# the results as in 2.
	68	# 2. Read a pre-prepared collation in one of a variety of formats,
	69	# and make the graph from that.
	70
	71	# The graph itself will (for now) be immutable, and the positions
	72	# within the graph will also be immutable. We need to calculate those
	73	# positions upon graph construction. The equivalences between graph
	74	# nodes will be mutable, entirely determined by the user (or possibly
	75	# by some semantic pre-processing provided by the user.) So the
	76	# constructor should just make an empty equivalences object. The
	77	# constructor will also need to make the witness objects, if we didn't
	78	# come through option 1.
	79
d047cd52	80	sub BUILD {
d047cd52	81	my( $self, $args ) = @_;
8e1394aa	82	$self->graph->use_class('node', 'Text::Tradition::Collation::Reading');
d047cd52	83
4a8828f0	84	# Pass through any graph-specific options.
	85	my $shape = exists( $args->{'shape'} ) ? $args->{'shape'} : 'ellipse';
	86	$self->graph->set_attribute( 'node', 'shape', $shape );
d047cd52	87	}
784877d9	88
de51424a	89	# Wrappes around merge_nodes
784877d9	90
	91	sub merge_readings {
	92	my $self = shift;
	93	my $first_node = shift;
	94	my $second_node = shift;
	95	$first_node->merge_from( $second_node );
	96	unshift( @_, $first_node, $second_node );
	97	return $self->graph->merge_nodes( @_ );
	98	}
	99
8e1394aa	100	=head2 Output method(s)
	101
	102	=over
	103
	104	=item B<as_svg>
	105
	106	print $graph->as_svg( $recalculate );
	107
	108	Returns an SVG string that represents the graph. Uses GraphViz to do
4a8828f0	109	this, because Graph::Easy doesn\'t cope well with long graphs. Unless
8e1394aa	110	$recalculate is passed (and is a true value), the method will return a
	111	cached copy of the SVG after the first call to the method.
	112
	113	=cut
	114
	115	sub as_svg {
	116	my( $self, $recalc ) = @_;
	117	return $self->svg if $self->has_svg;
	118
	119	$self->_save_graphviz( $self->graph->as_graphviz() )
	120	unless( $self->has_graphviz && !$recalc );
	121
	122	my @cmd = qw/dot -Tsvg/;
	123	my( $svg, $err );
	124	my $in = $self->graphviz;
	125	run( \@cmd, \$in, ">", binary(), \$svg );
	126	$self->{'svg'} = $svg;
	127	return $svg;
	128	}
	129
	130	=item B<as_graphml>
	131
	132	print $graph->as_graphml( $recalculate )
	133
	134	Returns a GraphML representation of the collation graph, with
	135	transposition information and position information. Unless
	136	$recalculate is passed (and is a true value), the method will return a
	137	cached copy of the SVG after the first call to the method.
	138
	139	=cut
	140
	141	sub as_graphml {
	142	my( $self, $recalc ) = @_;
	143	return $self->graphml if $self->has_graphml;
	144
	145	# Some namespaces
	146	my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
	147	my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
	148	my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
	149	'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
	150
	151	# Create the document and root node
	152	my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
	153	my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
	154	$graphml->setDocumentElement( $root );
	155	$root->setNamespace( $xsi_ns, 'xsi', 0 );
	156	$root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
	157
	158	# Add the data keys for nodes
	159	my @node_data = ( 'name', 'token', 'identical', 'position' );
	160	foreach my $ndi ( 0 .. $#node_data ) {
	161	my $key = $root->addNewChild( $graphml_ns, 'key' );
	162	$key->setAttribute( 'attr.name', $node_data[$ndi] );
	163	$key->setAttribute( 'attr.type', 'string' );
	164	$key->setAttribute( 'for', 'node' );
	165	$key->setAttribute( 'id', 'd'.$ndi );
	166	}
	167
	168	# Add the data keys for edges
	169	my %wit_hash;
	170	my $wit_ctr = 0;
	171	foreach my $wit ( $self->getWitnessList ) {
	172	my $wit_key = 'w' . $wit_ctr++;
	173	$wit_hash{$wit} = $wit_key;
174	my $key = $root->addNewChild( $graphml_ns, 'key' );
175	$key->setAttribute( 'attr.name', $wit );
176	$key->setAttribute( 'attr.type', 'string' );
177	$key->setAttribute( 'for', 'edge' );
178	$key->setAttribute( 'id', $wit_key );
179	}
180
181	# Add the graph, its nodes, and its edges
182	my $graph = $root->addNewChild( $graphml_ns, 'graph' );
183	$graph->setAttribute( 'edgedefault', 'directed' );
184	$graph->setAttribute( 'id', 'g0' ); # TODO make this meaningful
185	$graph->setAttribute( 'parse.edgeids', 'canonical' );
186	$graph->setAttribute( 'parse.edges', $self->edges() );
187	$graph->setAttribute( 'parse.nodeids', 'canonical' );
188	$graph->setAttribute( 'parse.nodes', $self->nodes() );
189	$graph->setAttribute( 'parse.order', 'nodesfirst' );
190
191	my $node_ctr = 0;
192	my %node_hash;
193	foreach my $n ( $self->readings ) {
194	my %this_node_data = ();
195	foreach my $ndi ( 0 .. $#node_data ) {
196	my $value;
197	$this_node_data{'d'.$ndi} = $n->name if $node_data[$ndi] eq 'name';
198	$this_node_data{'d'.$ndi} = $n->label
199	if $node_data[$ndi] eq 'token';
200	$this_node_data{'d'.$ndi} = $n->primary->name if $n->has_primary;
201	$this_node_data{'d'.$ndi} =
202	$self->{'positions'}->node_position( $n )
203	if $node_data[$ndi] eq 'position';
204	}
205	my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
206	my $node_xmlid = 'n' . $node_ctr++;
207	$node_hash{ $n->name } = $node_xmlid;
208	$node_el->setAttribute( 'id', $node_xmlid );
209
210	foreach my $dk ( keys %this_node_data ) {
211	my $d_el = $node_el->addNewChild( $graphml_ns, 'data' );
212	$d_el->setAttribute( 'key', $dk );
213	$d_el->appendTextChild( $this_node_data{$dk} );
214	}
215	}
216
217	foreach my $e ( $self->edges() ) {
218	my( $name, $from, $to ) = ( $e->name,
219	$node_hash{ $e->from()->name() },
220	$node_hash{ $e->to()->name() } );
221	my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
222	$edge_el->setAttribute( 'source', $from );
223	$edge_el->setAttribute( 'target', $to );
224	$edge_el->setAttribute( 'id', $name );
225	# TODO Got to add the witnesses
226	}
227
228	# Return the thing
229	$self->_save_graphml( $graphml );
230	return $graphml;
231	}
232
233	=back
234
de51424a	235	=head2 Navigation methods
	236
	237	=over
	238
8e1394aa	239	=item B<start>
	240
	241	my $beginning = $collation->start();
	242
	243	Returns the beginning of the collation, a meta-reading with label '#START#'.
	244
	245	=cut
	246
	247	sub start {
4a8828f0	248	# Return the beginning reading of the graph.
8e1394aa	249	my $self = shift;
	250	my( $new_start ) = @_;
	251	if( $new_start ) {
	252	$self->del_reading( '#START#' );
	253	$self->graph->rename_node( $new_start, '#START#' );
	254	}
	255	return $self->reading('#START#');
	256	}
	257
4a8828f0	258	=item B<next_reading>
8e1394aa	259
4a8828f0	260	my $next_reading = $graph->next_reading( $reading, $witpath );
8e1394aa	261
4a8828f0	262	Returns the reading that follows the given reading along the given witness
8e1394aa	263	path. TODO These are badly named.
	264
	265	=cut
	266
4a8828f0	267	sub next_reading {
8e1394aa	268	# Return the successor via the corresponding edge.
8e1394aa	269	my $self = shift;
4a8828f0	270	return $self->_find_linked_reading( 'next', @_ );
8e1394aa	271	}
8e1394aa	272
4a8828f0	273	=item B<prior_reading>
8e1394aa	274
4a8828f0	275	my $prior_reading = $graph->prior_reading( $reading, $witpath );
8e1394aa	276
4a8828f0	277	Returns the reading that precedes the given reading along the given witness
8e1394aa	278	path. TODO These are badly named.
	279
	280	=cut
	281
4a8828f0	282	sub prior_reading {
8e1394aa	283	# Return the predecessor via the corresponding edge.
8e1394aa	284	my $self = shift;
4a8828f0	285	return $self->_find_linked_reading( 'prior', @_ );
8e1394aa	286	}
8e1394aa	287
4a8828f0	288	sub _find_linked_reading {
8e1394aa	289	my( $self, $direction, $node, $edge ) = @_;
	290	$edge = 'base text' unless $edge;
	291	my @linked_edges = $direction eq 'next'
	292	? $node->outgoing() : $node->incoming();
	293	return undef unless scalar( @linked_edges );
	294
	295	# We have to find the linked edge that contains all of the
	296	# witnesses supplied in $edge.
4a8828f0	297	my @edge_wits = $self->witnesses_of_label( $edge );
8e1394aa	298	foreach my $le ( @linked_edges ) {
4a8828f0	299	my @le_wits = $self->witnesses_of_label( $le->name );
8e1394aa	300	if( _is_within( \@edge_wits, \@le_wits ) ) {
	301	# This is the right edge.
	302	return $direction eq 'next' ? $le->to() : $le->from();
	303	}
	304	}
	305	warn "Could not find $direction node from " . $node->label
	306	. " along edge $edge";
	307	return undef;
	308	}
	309
4a8828f0	310	# Some set logic.
	311	sub _is_within {
	312	my( $set1, $set2 ) = @_;
	313	my $ret = 1;
	314	foreach my $el ( @$set1 ) {
	315	$ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
	316	}
	317	return $ret;
	318	}
	319
de51424a	320
de51424a	321	## INITIALIZATION METHODS - for use by parsers
4a8828f0	322	# Walk the paths for each witness in the graph, and return the nodes
	323	# that the graph has in common.
	324
	325	sub walk_witness_paths {
	326	my( $self, $end ) = @_;
	327	# For each witness, walk the path through the graph.
	328	# Then we need to find the common nodes.
	329	# TODO This method is going to fall down if we have a very gappy
	330	# text in the collation.
	331	my $paths = {};
3a1f2523	332	my @common_readings;
4a8828f0	333	foreach my $wit ( @{$self->tradition->witnesses} ) {
	334	my $curr_reading = $self->start;
	335	my @wit_path = ( $curr_reading );
	336	my %seen_readings;
	337	# TODO Detect loops at some point
	338	while( $curr_reading->name ne $end->name ) {
	339	if( $seen_readings{$curr_reading->name} ) {
	340	warn "Detected loop walking path for witness " . $wit->sigil
	341	. " at reading " . $curr_reading->name;
	342	last;
	343	}
	344	my $next_reading = $self->next_reading( $curr_reading,
	345	$wit->sigil );
	346	push( @wit_path, $next_reading );
	347	$seen_readings{$curr_reading->name} = 1;
	348	$curr_reading = $next_reading;
	349	}
	350	$wit->path( \@wit_path );
3a1f2523	351	if( @common_readings ) {
4a8828f0	352	my @cn;
4a8828f0	353	foreach my $n ( @wit_path ) {
3a1f2523	354	push( @cn, $n ) if grep { $_ eq $n } @common_readings;
4a8828f0	355	}
3a1f2523	356	@common_readings = ();
3a1f2523	357	push( @common_readings, @cn );
4a8828f0	358	} else {
3a1f2523	359	push( @common_readings, @wit_path );
4a8828f0	360	}
	361	}
	362
	363	# Mark all the nodes as either common or not.
3a1f2523	364	foreach my $cn ( @common_readings ) {
de51424a	365	print STDERR "Setting " . $cn->name . " / " . $cn->label . " as common node\n";
4a8828f0	366	$cn->make_common;
	367	}
	368	foreach my $n ( $self->readings() ) {
	369	$n->make_variant unless $n->is_common;
	370	}
3a1f2523	371	# Return an array of the common nodes in order.
3a1f2523	372	return @common_readings;
4a8828f0	373	}
	374
	375	sub common_readings {
	376	my $self = shift;
	377	my @common = grep { $_->is_common } $self->readings();
de51424a	378	return sort { _cmp_position( $a->position, $b->position ) } @common;
4a8828f0	379	}
	380
	381	# Calculate the relative positions of nodes in the graph, if they
	382	# were not given to us.
	383	sub calculate_positions {
3a1f2523	384	my( $self, @ordered_common ) = @_;
4a8828f0	385
	386	# We have to calculate the position identifiers for each word,
	387	# keyed on the common nodes. This will be 'fun'. The end result
	388	# is a hash per witness, whose key is the word node and whose
	389	# value is its position in the text. Common nodes are always N,1
	390	# so have identical positions in each text.
4a8828f0	391
	392	my $node_pos = {};
	393	foreach my $wit ( @{$self->tradition->witnesses} ) {
	394	# First we walk each path, making a matrix for each witness that
	395	# corresponds to its eventual position identifier. Common nodes
	396	# always start a new row, and are thus always in the first column.
	397
	398	my $wit_matrix = [];
	399	my $cn = 0; # We should hit the common readings in order.
	400	my $row = [];
	401	foreach my $wn ( @{$wit->path} ) {
3a1f2523	402	if( $wn eq $ordered_common[$cn] ) {
4a8828f0	403	# Set up to look for the next common node, and
	404	# start a new row of words.
	405	$cn++;
	406	push( @$wit_matrix, $row ) if scalar( @$row );
	407	$row = [];
	408	}
	409	push( @$row, $wn );
	410	}
	411	push( @$wit_matrix, $row ); # Push the last row onto the matrix
	412
	413	# Now we have a matrix per witness, so that each row in the
	414	# matrix begins with a common node, and continues with all the
	415	# variant words that appear in the witness. We turn this into
	416	# real positions in row,cell format. But we need some
	417	# trickery in order to make sure that each node gets assigned
	418	# to only one position.
	419
	420	foreach my $li ( 1..scalar(@$wit_matrix) ) {
	421	foreach my $di ( 1..scalar(@{$wit_matrix->[$li-1]}) ) {
	422	my $reading = $wit_matrix->[$li-1]->[$di-1];
	423	my $position = "$li,$di";
	424	# If we have seen this node before, we need to compare
	425	# its position with what went before.
	426	unless( $reading->has_position &&
	427	_cmp_position( $position, $reading->position ) < 1 ) {
	428	# The new position ID replaces the old one.
	429	$reading->position( $position );
	430	} # otherwise, the old position needs to stay.
	431	}
	432	}
	433	}
3a1f2523	434
3a1f2523	435	$self->init_lemmata();
4a8828f0	436	}
	437
	438	sub _cmp_position {
	439	my( $a, $b ) = @_;
de51424a	440	if ( $a && $b ) {
	441	my @pos_a = split(/,/, $a );
	442	my @pos_b = split(/,/, $b );
	443
	444	my $big_cmp = $pos_a[0] <=> $pos_b[0];
	445	return $big_cmp if $big_cmp;
	446	# else
	447	return $pos_a[1] <=> $pos_b[1];
	448	} elsif ( $b ) { # a is undefined
	449	return -1;
	450	} elsif ( $a ) { # b is undefined
	451	return 1;
	452	}
	453	return 0; # they are both undefined
8e1394aa	454	}
3a1f2523	455
	456	sub all_positions {
	457	my $self = shift;
	458	my %positions = ();
	459	map { $positions{$_->position} = 1 } $self->readings;
de51424a	460	my @answer = sort { _cmp_position( $a, $b ) } keys( %positions );
de51424a	461	return @answer;
3a1f2523	462	}
	463
	464	sub readings_at_position {
	465	my( $self, $pos ) = @_;
	466	my @answer = grep { $_->position eq $pos } $self->readings;
	467	return @answer;
	468	}
	469
	470	## Lemmatizer functions
	471
	472	sub init_lemmata {
	473	my $self = shift;
	474
	475	foreach my $position ( $self->all_positions ) {
	476	$self->lemmata->{$position} = undef;
	477	}
	478
	479	foreach my $cr ( $self->common_readings ) {
	480	$self->lemmata->{$cr->position} = $cr->name;
	481	}
	482	}
	483
	484	=item B<lemma_readings>
	485
	486	my @state = $graph->lemma_readings( @readings_delemmatized );
	487
	488	Takes a list of readings that have just been delemmatized, and returns
	489	a set of tuples of the form ['reading', 'state'] that indicates what
	490	changes need to be made to the graph.
	491
	492	=over
	493
	494	=item *
	495
	496	A state of 1 means 'lemmatize this reading'
	497
	498	=item *
	499
	500	A state of 0 means 'delemmatize this reading'
	501
	502	=item *
	503
	504	A state of undef means 'an ellipsis belongs in the text here because
	505	no decision has been made / an earlier decision was backed out'
	506
	507	=back
	508
	509	=cut
	510
	511	sub lemma_readings {
	512	my( $self, @toggled_off_nodes ) = @_;
	513
	514	# First get the positions of those nodes which have been
	515	# toggled off.
	516	my $positions_off = {};
	517	map { $positions_off->{ $_->position } = $_->name } @toggled_off_nodes;
de51424a	518
3a1f2523	519	# Now for each position, we have to see if a node is on, and we
	520	# have to see if a node has been turned off.
	521	my @answer;
	522	foreach my $pos ( $self->all_positions() ) {
	523	# Find the state of this position. If there is an active node,
	524	# its name will be the state; otherwise the state will be 0
	525	# (nothing at this position) or undef (ellipsis at this position)
	526	my $active = $self->lemmata->{$pos};
	527
	528	# Is there a formerly active node that was toggled off?
	529	if( exists( $positions_off->{$pos} ) ) {
	530	my $off_node = $positions_off->{$pos};
	531	if( $active && $active ne $off_node) {
	532	push( @answer, [ $off_node, 0 ], [ $active, 1 ] );
	533	} else {
	534	push( @answer, [ $off_node, $active ] );
	535	}
	536
	537	# No formerly active node, so we just see if there is a currently
	538	# active one.
	539	} elsif( $active ) {
	540	# Push the active node, whatever it is.
	541	push( @answer, [ $active, 1 ] );
	542	} else {
	543	# Push the state that is there. Arbitrarily use the first node
	544	# at that position.
	545	my @pos_nodes = $self->readings_at_position( $pos );
de51424a	546	push( @answer, [ $pos_nodes[0]->name, $self->lemmata->{$pos} ] );
3a1f2523	547	}
	548	}
	549
	550	return @answer;
	551	}
	552
de51424a	553	=item B<toggle_reading>
	554
	555	my @readings_delemmatized = $graph->toggle_reading( $reading_name );
	556
	557	Takes a reading node name, and either lemmatizes or de-lemmatizes
	558	it. Returns a list of all readings that are de-lemmatized as a result
	559	of the toggle.
	560
	561	=cut
	562
	563	sub toggle_reading {
	564	my( $self, $rname ) = @_;
	565
	566	return unless $rname;
	567	my $reading = $self->reading( $rname );
	568	if( !$reading \|\| $reading->is_common() ) {
	569	# Do nothing, it's a common node.
	570	return;
	571	}
	572
	573	my $pos = $reading->position;
	574	my $old_state = $self->lemmata->{$pos};
	575	my @readings_off;
	576	if( $old_state && $old_state eq $rname ) {
	577	# Turn off the node. We turn on no others by default.
	578	push( @readings_off, $reading );
	579	} else {
	580	# Turn on the node.
	581	$self->lemmata->{$pos} = $rname;
	582	# Any other 'on' readings in the same position should be off.
	583	push( @readings_off, $self->same_position_as( $reading ) );
	584	# Any node that is an identical transposed one should be off.
	585	push( @readings_off, $reading->identical_readings );
	586	}
	587	@readings_off = unique_list( @readings_off );
	588
	589	# Turn off the readings that need to be turned off.
	590	my @readings_delemmatized;
	591	foreach my $n ( @readings_off ) {
	592	my $state = $self->lemmata->{$n->position};
	593	if( $state && $state eq $n->name ) {
	594	# this reading is still on, so turn it off
	595	push( @readings_delemmatized, $n );
	596	my $new_state = undef;
	597	if( $n eq $reading ) {
	598	# This is the reading that was clicked, so if there are no
	599	# other readings there, turn off the position. In all other
	600	# cases, restore the ellipsis.
	601	my @other_n = $self->same_position_as( $n );
	602	$new_state = 0 unless @other_n;
	603	}
	604	$self->lemmata->{$n->position} = $new_state;
	605	} elsif( $old_state && $old_state eq $n->name ) {
	606	# another reading has already been turned on here
	607	push( @readings_delemmatized, $n );
	608	} # else some other reading was on anyway, so pass.
	609	}
	610	return @readings_delemmatized;
	611	}
	612
	613	sub same_position_as {
	614	my( $self, $reading ) = @_;
	615	my $pos = $reading->position;
	616	my @same = grep { $_ ne $reading } $self->readings_at_position( $reading->position );
617	return @same;
618	}
3a1f2523	619
4a8828f0	620	# Return the string that joins together a list of witnesses for
	621	# display on a single path.
	622	sub path_label {
	623	my $self = shift;
	624	return join( $self->wit_list_separator, @_ );
	625	}
	626
	627	sub witnesses_of_label {
de51424a	628	my( $self, $label ) = @_;
4a8828f0	629	my $regex = $self->wit_list_separator;
de51424a	630	my @answer = split( /\Q$regex\E/, $label );
de51424a	631	return @answer;
4a8828f0	632	}
8e1394aa	633
de51424a	634	sub unique_list {
	635	my( @list ) = @_;
	636	my %h;
	637	map { $h{$_->name} = $_ } @list;
	638	return values( %h );
	639	}
	640
dd3b58b0	641	no Moose;
dd3b58b0	642	__PACKAGE__->meta->make_immutable;