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

package Text::Tradition::Stemma;

use Bio::Phylo::IO;
use Encode qw( decode_utf8 );
use File::chdir;
use File::Temp;
use File::Which;
use Graph;
use Graph::Reader::Dot;
use IPC::Run qw/ run binary /;
use Moose;

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

has graph => (
    is => 'rw',
    isa => 'Graph',
    predicate => 'has_graph',
    );
    
has distance_trees => (
    is => 'ro',
    isa => 'ArrayRef[Graph]',
    writer => '_save_distance_trees',
    predicate => 'has_distance_trees',
    );
    
sub BUILD {
    my( $self, $args ) = @_;
    # If we have been handed a dotfile, initialize it into a graph.
    if( exists $args->{'dot'} ) {
        $self->graph_from_dot( $args->{'dot'} );
    }
}

sub graph_from_dot {
	my( $self, $dotfh ) = @_;
	# Assume utf-8
	binmode( $dotfh, ':utf8' );
 	my $reader = Graph::Reader::Dot->new();
	my $graph = $reader->read_graph( $dotfh );
	if( $graph ) {
		$self->graph( $graph );
		# Go through the nodes and set any non-hypothetical node to extant.
		foreach my $v ( $self->graph->vertices ) {
			$self->graph->set_vertex_attribute( $v, 'class', 'extant' )
				unless $self->graph->has_vertex_attribute( $v, 'class' );
		}
	} else {
		warn "Failed to parse dot in $dotfh";
	}
}

sub as_dot {
    my( $self, $opts ) = @_;
    
    # Get default and specified options
    my %graphopts = ();
    my %nodeopts = (
		'fontsize' => 11,
		'hshape' => 'plaintext',	# Shape for the hypothetical nodes
		'htext' => '*',
		'style' => 'filled',
		'fillcolor' => 'white',
		'shape' => 'ellipse',	# Shape for the extant nodes
	);
	my %edgeopts = (
		'arrowhead' => 'open',
	);
	@graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}} 
		if $opts->{'graph'};
	@nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}} 
		if $opts->{'node'};
	@edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}} 
		if $opts->{'edge'};

	my @dotlines;
	push( @dotlines, 'digraph stemma {' );
	## Print out the global attributes
	push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
	push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
	## Delete our special attributes from the node set before continuing
	my $hshape = delete $nodeopts{'hshape'};
	my $htext = delete $nodeopts{'htext'};
	push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;

	# Add each of the nodes.
    foreach my $n ( $self->graph->vertices ) {
        if( $self->graph->get_vertex_attribute( $n, 'class' ) eq 'hypothetical' ) {
        	# Apply our display settings for hypothetical nodes.
        	push( @dotlines, _make_dotline( $n, 'shape' => $hshape, 'label' => $htext ) );
        } else {
        	# Use the default display settings.
            push( @dotlines, "  $n;" );
        }
    }
    # Add each of our edges.
    foreach my $e ( $self->graph->edges ) {
    	my( $from, $to ) = @$e;
    	push( @dotlines, "  $from -> $to;" );
    }
    push( @dotlines, '}' );
    
    return join( "\n", @dotlines );
}


# Another version of dot output meant for graph editing, thus
# much simpler.
sub editable {
	my $self = shift;
	my @dotlines;
	push( @dotlines, 'digraph stemma {' );
	my @real; # A cheap sort
    foreach my $n ( sort $self->graph->vertices ) {
    	my $c = $self->graph->get_vertex_attribute( $n, 'class' );
    	$c = 'extant' unless $c;
    	if( $c eq 'extant' ) {
    		push( @real, $n );
    	} else {
			push( @dotlines, _make_dotline( $n, 'class' => $c ) );
		}
    }
	# Now do the real ones
	foreach my $n ( @real ) {
		push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) );
	}
	foreach my $e ( sort _by_vertex $self->graph->edges ) {
		my( $from, $to ) = @$e;
		push( @dotlines, "  $from -> $to;" );
	}
    push( @dotlines, '}' );
    return join( "\n", @dotlines );
}

sub _make_dotline {
	my( $obj, %attr ) = @_;
	my @pairs;
	foreach my $k ( keys %attr ) {
		my $v = $attr{$k};
		$v =~ s/\"/\\\"/g;
		push( @pairs, "$k=\"$v\"" );
	}
	return sprintf( "  %s [ %s ];", $obj, join( ', ', @pairs ) );
}
	
sub _by_vertex {
	return $a->[0].$a->[1] cmp $b->[0].$b->[1];
}

# Render the stemma as SVG.
sub as_svg {
    my( $self, $opts ) = @_;
    my $dot = $self->as_dot( $opts );
    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 $dot;
    push( @cmd, $dotfile->filename );
    run( \@cmd, ">", binary(), \$svg );
    $svg = decode_utf8( $svg );
    return $svg;
}

sub witnesses {
    my $self = shift;
    my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' }
        $self->graph->vertices;
    return @wits;
}

#### Methods for calculating phylogenetic trees ####

before 'distance_trees' => sub {
    my $self = shift;
    my %args = @_;
    # TODO allow specification of method for calculating distance tree
    if( $args{'recalc'} || !$self->has_distance_trees ) {
        # We need to make a tree before we can return it.
        my( $ok, $result ) = $self->run_phylip_pars();
        if( $ok ) {
            # Save the resulting trees
            my $trees = _parse_newick( $result );
            $self->_save_distance_trees( $trees );
        } else {
            warn "Failed to calculate distance trees: $result";
        }
    }
};
        
sub make_character_matrix {
    my $self = shift;
    unless( $self->collation->linear ) {
        warn "Need a linear graph in order to make an alignment table";
        return;
    }
    my $table = $self->collation->make_alignment_table;
    # Push the names of the witnesses to initialize the rows of the matrix.
    my @matrix = map { [ $self->_normalize_ac( $_ ) ] } @{$table->[0]};
    foreach my $token_index ( 1 .. $#{$table} ) {
        # First implementation: make dumb alignment table, caring about
        # nothing except which reading is in which position.
        my @chars = convert_characters( $table->[$token_index] );
        foreach my $idx ( 0 .. $#matrix ) {
            push( @{$matrix[$idx]}, $chars[$idx] );
        }
    }
    return \@matrix;
} 

sub _normalize_ac {
    my( $self, $witname ) = @_;
    my $ac = $self->collation->ac_label;
    if( $witname =~ /(.*)\Q$ac\E$/ ) {
        $witname = $1 . '_ac';
    }
    return sprintf( "%-10s", $witname );
}

sub convert_characters {
    my $row = shift;
    # This is a simple algorithm that treats every reading as different.
    # Eventually we will want to be able to specify how relationships
    # affect the character matrix.
    my %unique = ( '__UNDEF__' => 'X',
                   '#LACUNA#'  => '?',
                 );
    my %count;
    my $ctr = 0;
    foreach my $word ( @$row ) {
        if( $word && !exists $unique{$word} ) {
            $unique{$word} = chr( 65 + $ctr );
            $ctr++;
        }
        $count{$word}++ if $word;
    }
    # Try to keep variants under 8 by lacunizing any singletons.
    if( scalar( keys %unique ) > 8 ) {
		foreach my $word ( keys %count ) {
			if( $count{$word} == 1 ) {
				$unique{$word} = '?';
			}
		}
    }
    my %u = reverse %unique;
    if( scalar( keys %u ) > 8 ) {
        warn "Have more than 8 variants on this location; phylip will break";
    }
    my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
    return @chars;
}

sub phylip_pars_input {
    my $self = shift;
    my $character_matrix = $self->make_character_matrix;
    my $input = '';
    my $rows = scalar @{$character_matrix};
    my $columns = scalar @{$character_matrix->[0]} - 1;
    $input .= "\t$rows\t$columns\n";
    foreach my $row ( @{$character_matrix} ) {
        $input .= join( '', @$row ) . "\n";
    }
    return $input;
}

sub run_phylip_pars {
    my $self = shift;

    # Set up a temporary directory for all the default Phylip files.
    my $phylip_dir = File::Temp->newdir();
    # $phylip_dir->unlink_on_destroy(0);
    # We need an infile, and we need a command input file.
    open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
    print MATRIX $self->phylip_pars_input();
    close MATRIX;

    open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
    ## TODO any configuration parameters we want to set here
#   U                 Search for best tree?  Yes
#   S                        Search option?  More thorough search
#   V              Number of trees to save?  100
#   J     Randomize input order of species?  No. Use input order
#   O                        Outgroup root?  No, use as outgroup species 1
#   T              Use Threshold parsimony?  No, use ordinary parsimony
#   W                       Sites weighted?  No
#   M           Analyze multiple data sets?  No
#   I            Input species interleaved?  Yes
#   0   Terminal type (IBM PC, ANSI, none)?  ANSI
#   1    Print out the data at start of run  No
#   2  Print indications of progress of run  Yes
#   3                        Print out tree  Yes
#   4          Print out steps in each site  No
#   5  Print character at all nodes of tree  No
#   6       Write out trees onto tree file?  Yes
    print CMD "Y\n";
    close CMD;

    # And then we run the program.
    my $program = File::Which::which( 'pars' );
    unless( -x $program ) {
	return( undef, "Phylip pars not found in path" );
    }

    {
        # We need to run it in our temporary directory where we have created
        # all the expected files.
        local $CWD = $phylip_dir;
        my @cmd = ( $program );
        run \@cmd, '<', 'cmdfile', '>', '/dev/null';
    }
    # Now our output should be in 'outfile' and our tree in 'outtree',
    # both in the temp directory.

    my @outtree;
    if( -f "$phylip_dir/outtree" ) {
        open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
        @outtree = <TREE>;
        close TREE;
    }
    return( 1, join( '', @outtree ) ) if @outtree;

    my @error;
    if( -f "$phylip_dir/outfile" ) {
        open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read";
        @error = <OUTPUT>;
        close OUTPUT;
    } else {
        push( @error, "Neither outtree nor output file was produced!" );
    }
    return( undef, join( '', @error ) );
}

sub _parse_newick {
    my $newick = shift;
    my @trees;
    # Parse the result into a tree
    my $forest = Bio::Phylo::IO->parse( 
        -format => 'newick',
        -string => $newick,
        );
    # Turn the tree into a graph, starting with the root node
    foreach my $tree ( @{$forest->get_entities} ) {
        push( @trees, _graph_from_bio( $tree ) );
    }
    return \@trees;
}

sub _graph_from_bio {
    my $tree = shift;
    my $graph = Graph->new( 'undirected' => 1 );
    # Give all the intermediate anonymous nodes a name.
    my $i = 0;
    foreach my $n ( @{$tree->get_entities} ) {
        next if $n->get_name;
        $n->set_name( $i++ );
    }
    my $root = $tree->get_root->get_name;
    $graph->add_vertex( $root );
    _add_tree_children( $graph, $root, $tree->get_root->get_children() );
    return $graph;
}

sub _add_tree_children {
    my( $graph, $parent, $tree_children ) = @_;
    foreach my $c ( @$tree_children ) {
        my $child = $c->get_name;
        $graph->add_vertex( $child );
        $graph->add_path( $parent, $child );
        _add_tree_children( $graph, $child, $c->get_children() );
    }
}

no Moose;
__PACKAGE__->meta->make_immutable;
    
1;
Commit	Line	Data
9463b0bf	1	package Text::Tradition::Stemma;
9463b0bf	2
40f19742	3	use Bio::Phylo::IO;
e79c23c7	4	use Encode qw( decode_utf8 );
9463b0bf	5	use File::chdir;
9463b0bf	6	use File::Temp;
457b1620	7	use File::Which;
e05997e2	8	use Graph;
e05997e2	9	use Graph::Reader::Dot;
e79c23c7	10	use IPC::Run qw/ run binary /;
40f19742	11	use Moose;
9463b0bf	12
	13	has collation => (
	14	is => 'ro',
	15	isa => 'Text::Tradition::Collation',
	16	required => 1,
8d9a1cd8	17	weak_ref => 1,
9463b0bf	18	);
9463b0bf	19
e05997e2	20	has graph => (
	21	is => 'rw',
	22	isa => 'Graph',
	23	predicate => 'has_graph',
	24	);
	25
40f19742	26	has distance_trees => (
	27	is => 'ro',
	28	isa => 'ArrayRef[Graph]',
	29	writer => '_save_distance_trees',
	30	predicate => 'has_distance_trees',
	31	);
c0ccdb62	32
e05997e2	33	sub BUILD {
	34	my( $self, $args ) = @_;
	35	# If we have been handed a dotfile, initialize it into a graph.
	36	if( exists $args->{'dot'} ) {
8d9a1cd8	37	$self->graph_from_dot( $args->{'dot'} );
e05997e2	38	}
c0ccdb62	39	}
c0ccdb62	40
8d9a1cd8	41	sub graph_from_dot {
	42	my( $self, $dotfh ) = @_;
	43	# Assume utf-8
	44	binmode( $dotfh, ':utf8' );
	45	my $reader = Graph::Reader::Dot->new();
	46	my $graph = $reader->read_graph( $dotfh );
7a7c249c	47	if( $graph ) {
	48	$self->graph( $graph );
	49	# Go through the nodes and set any non-hypothetical node to extant.
	50	foreach my $v ( $self->graph->vertices ) {
	51	$self->graph->set_vertex_attribute( $v, 'class', 'extant' )
	52	unless $self->graph->has_vertex_attribute( $v, 'class' );
	53	}
	54	} else {
	55	warn "Failed to parse dot in $dotfh";
	56	}
8d9a1cd8	57	}
	58
	59	sub as_dot {
e367f5c0	60	my( $self, $opts ) = @_;
7a7c249c	61
	62	# Get default and specified options
	63	my %graphopts = ();
	64	my %nodeopts = (
	65	'fontsize' => 11,
	66	'hshape' => 'plaintext', # Shape for the hypothetical nodes
	67	'htext' => '*',
	68	'style' => 'filled',
	69	'fillcolor' => 'white',
	70	'shape' => 'ellipse', # Shape for the extant nodes
	71	);
	72	my %edgeopts = (
	73	'arrowhead' => 'open',
	74	);
	75	@graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}}
	76	if $opts->{'graph'};
	77	@nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}}
	78	if $opts->{'node'};
	79	@edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}}
	80	if $opts->{'edge'};
	81
	82	my @dotlines;
	83	push( @dotlines, 'digraph stemma {' );
	84	## Print out the global attributes
	85	push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
	86	push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
	87	## Delete our special attributes from the node set before continuing
	88	my $hshape = delete $nodeopts{'hshape'};
	89	my $htext = delete $nodeopts{'htext'};
	90	push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;
	91
	92	# Add each of the nodes.
	93	foreach my $n ( $self->graph->vertices ) {
	94	if( $self->graph->get_vertex_attribute( $n, 'class' ) eq 'hypothetical' ) {
	95	# Apply our display settings for hypothetical nodes.
	96	push( @dotlines, _make_dotline( $n, 'shape' => $hshape, 'label' => $htext ) );
e79c23c7	97	} else {
7a7c249c	98	# Use the default display settings.
7a7c249c	99	push( @dotlines, " $n;" );
e79c23c7	100	}
e79c23c7	101	}
7a7c249c	102	# Add each of our edges.
	103	foreach my $e ( $self->graph->edges ) {
	104	my( $from, $to ) = @$e;
	105	push( @dotlines, " $from -> $to;" );
	106	}
	107	push( @dotlines, '}' );
e79c23c7	108
7a7c249c	109	return join( "\n", @dotlines );
	110	}
	111
	112
	113	# Another version of dot output meant for graph editing, thus
	114	# much simpler.
	115	sub editable {
	116	my $self = shift;
	117	my @dotlines;
	118	push( @dotlines, 'digraph stemma {' );
	119	my @real; # A cheap sort
	120	foreach my $n ( sort $self->graph->vertices ) {
	121	my $c = $self->graph->get_vertex_attribute( $n, 'class' );
	122	$c = 'extant' unless $c;
	123	if( $c eq 'extant' ) {
	124	push( @real, $n );
	125	} else {
	126	push( @dotlines, _make_dotline( $n, 'class' => $c ) );
	127	}
e367f5c0	128	}
7a7c249c	129	# Now do the real ones
	130	foreach my $n ( @real ) {
	131	push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) );
	132	}
	133	foreach my $e ( sort _by_vertex $self->graph->edges ) {
	134	my( $from, $to ) = @$e;
	135	push( @dotlines, " $from -> $to;" );
	136	}
	137	push( @dotlines, '}' );
	138	return join( "\n", @dotlines );
	139	}
	140
	141	sub _make_dotline {
	142	my( $obj, %attr ) = @_;
	143	my @pairs;
	144	foreach my $k ( keys %attr ) {
	145	my $v = $attr{$k};
	146	$v =~ s/\"/\\\"/g;
	147	push( @pairs, "$k=\"$v\"" );
	148	}
	149	return sprintf( " %s [ %s ];", $obj, join( ', ', @pairs ) );
8d9a1cd8	150	}
8d9a1cd8	151
7a7c249c	152	sub _by_vertex {
	153	return $a->[0].$a->[1] cmp $b->[0].$b->[1];
	154	}
8d9a1cd8	155
	156	# Render the stemma as SVG.
	157	sub as_svg {
	158	my( $self, $opts ) = @_;
	159	my $dot = $self->as_dot( $opts );
e79c23c7	160	my @cmd = qw/dot -Tsvg/;
	161	my( $svg, $err );
	162	my $dotfile = File::Temp->new();
	163	## TODO REMOVE
	164	# $dotfile->unlink_on_destroy(0);
	165	binmode $dotfile, ':utf8';
8d9a1cd8	166	print $dotfile $dot;
e79c23c7	167	push( @cmd, $dotfile->filename );
	168	run( \@cmd, ">", binary(), \$svg );
	169	$svg = decode_utf8( $svg );
	170	return $svg;
	171	}
	172
08e0fb85	173	sub witnesses {
	174	my $self = shift;
	175	my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' }
	176	$self->graph->vertices;
	177	return @wits;
	178	}
	179
e79c23c7	180	#### Methods for calculating phylogenetic trees ####
e79c23c7	181
40f19742	182	before 'distance_trees' => sub {
	183	my $self = shift;
	184	my %args = @_;
	185	# TODO allow specification of method for calculating distance tree
	186	if( $args{'recalc'} \|\| !$self->has_distance_trees ) {
	187	# We need to make a tree before we can return it.
	188	my( $ok, $result ) = $self->run_phylip_pars();
	189	if( $ok ) {
c0ccdb62	190	# Save the resulting trees
	191	my $trees = _parse_newick( $result );
	192	$self->_save_distance_trees( $trees );
40f19742	193	} else {
c0ccdb62	194	warn "Failed to calculate distance trees: $result";
40f19742	195	}
	196	}
	197	};
e05997e2	198
9463b0bf	199	sub make_character_matrix {
	200	my $self = shift;
	201	unless( $self->collation->linear ) {
910a0a6d	202	warn "Need a linear graph in order to make an alignment table";
910a0a6d	203	return;
9463b0bf	204	}
910a0a6d	205	my $table = $self->collation->make_alignment_table;
	206	# Push the names of the witnesses to initialize the rows of the matrix.
	207	my @matrix = map { [ $self->_normalize_ac( $_ ) ] } @{$table->[0]};
910a0a6d	208	foreach my $token_index ( 1 .. $#{$table} ) {
	209	# First implementation: make dumb alignment table, caring about
	210	# nothing except which reading is in which position.
	211	my @chars = convert_characters( $table->[$token_index] );
	212	foreach my $idx ( 0 .. $#matrix ) {
	213	push( @{$matrix[$idx]}, $chars[$idx] );
	214	}
9463b0bf	215	}
c0ccdb62	216	return \@matrix;
910a0a6d	217	}
9463b0bf	218
910a0a6d	219	sub _normalize_ac {
	220	my( $self, $witname ) = @_;
	221	my $ac = $self->collation->ac_label;
	222	if( $witname =~ /(.*)\Q$ac\E$/ ) {
	223	$witname = $1 . '_ac';
9463b0bf	224	}
910a0a6d	225	return sprintf( "%-10s", $witname );
9463b0bf	226	}
9463b0bf	227
910a0a6d	228	sub convert_characters {
910a0a6d	229	my $row = shift;
9463b0bf	230	# This is a simple algorithm that treats every reading as different.
	231	# Eventually we will want to be able to specify how relationships
	232	# affect the character matrix.
eca16057	233	my %unique = ( '__UNDEF__' => 'X',
	234	'#LACUNA#' => '?',
	235	);
a7fb3133	236	my %count;
910a0a6d	237	my $ctr = 0;
	238	foreach my $word ( @$row ) {
	239	if( $word && !exists $unique{$word} ) {
	240	$unique{$word} = chr( 65 + $ctr );
	241	$ctr++;
	242	}
a7fb3133	243	$count{$word}++ if $word;
9463b0bf	244	}
a7fb3133	245	# Try to keep variants under 8 by lacunizing any singletons.
910a0a6d	246	if( scalar( keys %unique ) > 8 ) {
a7fb3133	247	foreach my $word ( keys %count ) {
	248	if( $count{$word} == 1 ) {
	249	$unique{$word} = '?';
	250	}
	251	}
	252	}
	253	my %u = reverse %unique;
	254	if( scalar( keys %u ) > 8 ) {
40f19742	255	warn "Have more than 8 variants on this location; phylip will break";
910a0a6d	256	}
	257	my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
	258	return @chars;
9463b0bf	259	}
9463b0bf	260
40f19742	261	sub phylip_pars_input {
9463b0bf	262	my $self = shift;
c0ccdb62	263	my $character_matrix = $self->make_character_matrix;
	264	my $input = '';
	265	my $rows = scalar @{$character_matrix};
	266	my $columns = scalar @{$character_matrix->[0]} - 1;
	267	$input .= "\t$rows\t$columns\n";
	268	foreach my $row ( @{$character_matrix} ) {
	269	$input .= join( '', @$row ) . "\n";
f6066bac	270	}
c0ccdb62	271	return $input;
f6066bac	272	}
f6066bac	273
40f19742	274	sub run_phylip_pars {
f6066bac	275	my $self = shift;
9463b0bf	276
	277	# Set up a temporary directory for all the default Phylip files.
	278	my $phylip_dir = File::Temp->newdir();
eca16057	279	# $phylip_dir->unlink_on_destroy(0);
f6066bac	280	# We need an infile, and we need a command input file.
9463b0bf	281	open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
40f19742	282	print MATRIX $self->phylip_pars_input();
9463b0bf	283	close MATRIX;
	284
	285	open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
	286	## TODO any configuration parameters we want to set here
	287	# U Search for best tree? Yes
	288	# S Search option? More thorough search
	289	# V Number of trees to save? 100
	290	# J Randomize input order of species? No. Use input order
	291	# O Outgroup root? No, use as outgroup species 1
	292	# T Use Threshold parsimony? No, use ordinary parsimony
	293	# W Sites weighted? No
	294	# M Analyze multiple data sets? No
	295	# I Input species interleaved? Yes
	296	# 0 Terminal type (IBM PC, ANSI, none)? ANSI
	297	# 1 Print out the data at start of run No
	298	# 2 Print indications of progress of run Yes
	299	# 3 Print out tree Yes
	300	# 4 Print out steps in each site No
	301	# 5 Print character at all nodes of tree No
	302	# 6 Write out trees onto tree file? Yes
	303	print CMD "Y\n";
	304	close CMD;
	305
	306	# And then we run the program.
457b1620	307	my $program = File::Which::which( 'pars' );
	308	unless( -x $program ) {
	309	return( undef, "Phylip pars not found in path" );
9463b0bf	310	}
	311
	312	{
910a0a6d	313	# We need to run it in our temporary directory where we have created
	314	# all the expected files.
	315	local $CWD = $phylip_dir;
	316	my @cmd = ( $program );
	317	run \@cmd, '<', 'cmdfile', '>', '/dev/null';
9463b0bf	318	}
	319	# Now our output should be in 'outfile' and our tree in 'outtree',
	320	# both in the temp directory.
	321
	322	my @outtree;
	323	if( -f "$phylip_dir/outtree" ) {
910a0a6d	324	open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
	325	@outtree = <TREE>;
	326	close TREE;
9463b0bf	327	}
	328	return( 1, join( '', @outtree ) ) if @outtree;
	329
	330	my @error;
f6066bac	331	if( -f "$phylip_dir/outfile" ) {
910a0a6d	332	open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read";
	333	@error = <OUTPUT>;
	334	close OUTPUT;
9463b0bf	335	} else {
910a0a6d	336	push( @error, "Neither outtree nor output file was produced!" );
9463b0bf	337	}
	338	return( undef, join( '', @error ) );
	339	}
	340
40f19742	341	sub _parse_newick {
	342	my $newick = shift;
	343	my @trees;
	344	# Parse the result into a tree
	345	my $forest = Bio::Phylo::IO->parse(
	346	-format => 'newick',
	347	-string => $newick,
	348	);
	349	# Turn the tree into a graph, starting with the root node
	350	foreach my $tree ( @{$forest->get_entities} ) {
	351	push( @trees, _graph_from_bio( $tree ) );
	352	}
	353	return \@trees;
	354	}
	355
	356	sub _graph_from_bio {
	357	my $tree = shift;
	358	my $graph = Graph->new( 'undirected' => 1 );
	359	# Give all the intermediate anonymous nodes a name.
	360	my $i = 0;
	361	foreach my $n ( @{$tree->get_entities} ) {
	362	next if $n->get_name;
	363	$n->set_name( $i++ );
	364	}
	365	my $root = $tree->get_root->get_name;
	366	$graph->add_vertex( $root );
	367	_add_tree_children( $graph, $root, $tree->get_root->get_children() );
	368	return $graph;
	369	}
	370
	371	sub _add_tree_children {
	372	my( $graph, $parent, $tree_children ) = @_;
	373	foreach my $c ( @$tree_children ) {
	374	my $child = $c->get_name;
	375	$graph->add_vertex( $child );
	376	$graph->add_path( $parent, $child );
	377	_add_tree_children( $graph, $child, $c->get_children() );
	378	}
	379	}
	380
9463b0bf	381	no Moose;
	382	__PACKAGE__->meta->make_immutable;
	383
	384	1;