[scpubgit/stemmatology.git] / analysis / lib / Text / Tradition / StemmaUtil.pm

package Text::Tradition::StemmaUtil;

use strict;
use warnings;
use Exporter 'import';
use vars qw/ @EXPORT_OK /;
use Bio::Phylo::IO;
use Encode qw( decode_utf8 );
use File::chdir;
use File::Temp;
use File::Which;
use Graph;
use IPC::Run qw/ run binary /;
use Text::Tradition::Error;
@EXPORT_OK = qw/ display_graph editable_graph 
	character_input phylip_pars parse_newick newick_to_svg /;

=head1 NAME

Text::Tradition::StemmaUtil - standalone utilities for stemma graph display and
distance tree calculations

=head1 DESCRIPTION

This package contains a set of utilities for displaying arbitrary stemmata and 
running phylogenetic analysis on text collations.

=head1 SUBROUTINES

=head2 display_graph( $graph, $opts )

Returns a dot specification intended for display, according to the logical 
attributes of the witnesses.

=cut

sub display_graph {
    my( $graph, $opts ) = @_;
    
    # Get default and specified options
    my %graphopts = (
    	# 'ratio' => 1,
    	'bgcolor' => 'transparent',
    );
    my %nodeopts = (
		'fontsize' => 11,
		'style' => 'filled',
		'fillcolor' => 'white',
		'color' => 'white',
		'shape' => 'ellipse',	# Shape for the extant nodes
	);
	my %edgeopts = (
		'arrowhead' => 'none',
	);
	@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 $gdecl = $graph->is_directed ? 'digraph' : 'graph';
	my $gname = $opts->{'name'} ? '"' . $opts->{'name'} . '"'
		: 'stemma';
	my @dotlines;
	push( @dotlines, "$gdecl $gname {" );
	## Print out the global attributes
	push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
	push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
	push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;

	# Add each of the nodes.
    foreach my $n ( $graph->vertices ) {
    	my %vattr = ( 'id' => $n );  # Set the SVG element ID to the sigil itself
        if( $graph->has_vertex_attribute( $n, 'label' ) ) {
        	$vattr{'label'} = $graph->get_vertex_attribute( $n, 'label' );
        }
		push( @dotlines, _make_dotline( $n, %vattr ) );
    }
    # Add each of our edges.
    foreach my $e ( $graph->edges ) {
    	my( $from, $to ) = map { _dotquote( $_ ) } @$e;
    	my $connector = $graph->is_directed ? '->' : '--';
    	push( @dotlines, "  $from $connector $to;" );
    }
    push( @dotlines, '}' );
    
    return join( "\n", @dotlines );
}


=head2 editable_graph( $graph, $opts )

Returns a dot specification of a stemma graph with logical witness features,
intended for editing the stemma definition.

=cut

sub editable_graph {
	my( $graph, $opts ) = @_;

	# Create the graph
	my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n";
	my $fq = $opts->{'forcequote'};
	my $gdecl = $graph->is_undirected ? 'graph' : 'digraph';
	my $gname = exists $opts->{'name'} ? '"' . $opts->{'name'} . '"'
		: 'stemma';
	my @dotlines;
	push( @dotlines, "$gdecl $gname {" );
	my @real; # A cheap sort
    foreach my $n ( sort $graph->vertices ) {
    	my $c = $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, 'forcequote' => $fq ) );
		}
    }
	# Now do the real ones
	foreach my $n ( @real ) {
		push( @dotlines, _make_dotline( $n, 'class' => 'extant', 'forcequote' => $fq ) );
	}
	foreach my $e ( sort _by_vertex $graph->edges ) {
		my( $from, $to ) = map { _dotquote( $_ ) } @$e;
		my $conn = $graph->is_undirected ? '--' : '->';
		push( @dotlines, "  $from $conn $to;" );
	}
    push( @dotlines, '}' );
    return join( $join, @dotlines );
}

sub _make_dotline {
	my( $obj, %attr ) = @_;
	my @pairs;
	my $fq = delete $attr{forcequote};
	foreach my $k ( keys %attr ) {
		my $v = _dotquote( $attr{$k}, $fq );
		push( @pairs, "$k=$v" );
	}
	return sprintf( "  %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) );
}
	
sub _dotquote {
	my( $str, $force ) = @_;
	return $str if $str =~ /^[A-Za-z0-9]+$/;
	$str =~ s/\"/\\\"/g;
	$str = '"' . $str . '"';
	return $str;
}

sub _by_vertex {
	return $a->[0].$a->[1] cmp $b->[0].$b->[1];
}

=head2 character_input( $tradition, $opts )

Returns a character matrix string suitable for Phylip programs, which 
corresponds to the given alignment table.  See Text::Tradition::Collation 
for a description of the alignment table format. Options include:

=over

=item * exclude_layer - Exclude layered witnesses from the character input, 
using only the 'main' text of the witnesses in the tradition.

=item * collapse - A reference to an array of relationship names that should
be treated as equivalent for the purposes of generating the character matrix.

=back

=cut

sub character_input {
    my ( $tradition, $opts ) = @_;
    my $table = $tradition->collation->alignment_table;
    if( $opts->{exclude_layer} ) {
    	# Filter out all alignment table rows that do not correspond
    	# to a named witness - these are the layered witnesses.
    	my $newtable = { alignment => [], length => $table->{length} };
    	foreach my $row ( @{$table->{alignment}} ) {
    		if( $tradition->has_witness( $row->{witness} ) ) {
    			push( @{$newtable->{alignment}}, $row );
    		}
    	}
    	$table = $newtable;
    }
    my $character_matrix = _make_character_matrix( $table, $opts );
    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 _make_character_matrix {
    my( $table, $opts ) = @_;
    # Push the names of the witnesses to initialize the rows of the matrix.
    my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] } 
    				@{$table->{'alignment'}};
    foreach my $token_index ( 0 .. $table->{'length'} - 1) {
        my @pos_tokens = map { $_->{'tokens'}->[$token_index] }
        						@{$table->{'alignment'}};
        my @pos_readings = map { $_ ? $_->{'t'} : $_ } @pos_tokens;
        my @chars = _convert_characters( \@pos_readings, $opts );
        foreach my $idx ( 0 .. $#matrix ) {
            push( @{$matrix[$idx]}, $chars[$idx] );
        }
    }
    return \@matrix;
} 

# Helper function to make the witness name something legal for pars

sub _normalize_witname {
    my( $witname ) = @_;
    $witname =~ s/\s+/ /g;
    $witname =~ s/[\[\]\(\)\:;,]//g;
    $witname = substr( $witname, 0, 10 );
    return sprintf( "%-10s", $witname );
}

sub _convert_characters {
    my( $row, $opts ) = @_;
    # 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 %equivalent;
    my %count;
    my $ctr = 0;
    foreach my $rdg ( @$row ) {
    	next unless $rdg;
    	next if $rdg->is_lacuna;
		next if exists $unique{$rdg->text};
		if( ref( $opts->{'collapse'} ) eq 'ARRAY' ) {
			my @exclude_types = @{$opts->{'collapse'}};
			my @set = $rdg->related_readings( sub { my $rel = shift;
				$rel->colocated && grep { $rel->type eq $_ } @exclude_types } );
			push( @set, $rdg );
			my $char = chr( 65 + $ctr++ );
			map { $unique{$_->text} = $char } @set;
			$count{$rdg->text} += scalar @set;
		} else {
			$unique{$rdg->text} = chr( 65 + $ctr++ );
			$count{$rdg->text}++;			
		}
    }
    # 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 { $_ ? $unique{$_->text} : $unique{'__UNDEF__' } } @$row;
    return @chars;
}

=head2 phylip_pars( $character_matrix )

Runs Phylip Pars on the given character matrix.  Returns results in Newick format.

=cut

sub phylip_pars {
	my( $charmatrix ) = @_;
    # 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 $charmatrix;
    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( $program && -x $program ) {
		throw( "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 join( '', @outtree ) if @outtree;

	# If we got this far, we are about to throw an error.
    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!" );
    }
    throw( join( '', @error ) );
}

=head2 parse_newick( $newick_string )

Parses the given Newick tree(s) into one or more Stemma objects with
undirected graphs.

=cut

sub parse_newick {
    my $newick = shift;
    # Parse the result into a set of trees and return them.
    my $forest = Bio::Phylo::IO->parse( 
        -format => 'newick',
        -string => $newick,
        );
    return map { _graph_from_bio( $_ ) } @{$forest->get_entities};
}

sub _graph_from_bio {
    my $tree = shift;
    my $graph = Graph->new( 'undirected' => 1 );
    # Give all the intermediate anonymous nodes a name.
    my $i = 0;
    my $classes = {};
    foreach my $n ( @{$tree->get_terminals} ) {
    	# The terminal nodes are our named witnesses.
		$classes->{$n->get_name} = 'extant';
	}
	foreach my $n ( @{$tree->get_internals} ) {
    	unless( defined $n->get_name && $n->get_name ne '' ) {
    		# Get an integer, make sure it's a unique name
    		while( exists $classes->{$i} ) {
    			$i++;
    		}
    		$n->set_name( $i++ );
    	}
    	$classes->{$n->get_name} = 'hypothetical';
    }
    _add_tree_children( $graph, $classes, undef, [ $tree->get_root ]);
    return $graph;
}

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

=head2 newick_to_svg( $newick_string )

Uses the FigTree utility (if installed) to transform the given Newick tree(s)
into a graph visualization.

=cut

sub newick_to_svg {
	my $newick = shift;
    my $program = File::Which::which( 'figtree' );
    unless( -x $program ) {
		throw( "FigTree commandline utility not found in path" );
    }
    my $svg;
    my $nfile = File::Temp->new();
    print $nfile $newick;
    close $nfile;
	my @cmd = ( $program, '-graphic', 'SVG', $nfile );
    run( \@cmd, ">", binary(), \$svg );
    return decode_utf8( $svg );
}

sub throw {
	Text::Tradition::Error->throw( 
		'ident' => 'StemmaUtil error',
		'message' => $_[0],
		);
}

1;

=head1 LICENSE

This package is free software and is provided "as is" without express
or implied warranty.  You can redistribute it and/or modify it under
the same terms as Perl itself.

=head1 AUTHOR

Tara L Andrews E<lt>aurum@cpan.orgE<gt>
Commit	Line	Data
68454b71	1	package Text::Tradition::StemmaUtil;
	2
	3	use strict;
	4	use warnings;
	5	use Exporter 'import';
	6	use vars qw/ @EXPORT_OK /;
b02332ca	7	use Bio::Phylo::IO;
27e2a8fe	8	use Encode qw( decode_utf8 );
b02332ca	9	use File::chdir;
	10	use File::Temp;
	11	use File::Which;
	12	use Graph;
b02332ca	13	use IPC::Run qw/ run binary /;
edac47cc	14	use Text::Tradition::Error;
5873cf38	15	@EXPORT_OK = qw/ display_graph editable_graph
5873cf38	16	character_input phylip_pars parse_newick newick_to_svg /;
68454b71	17
027d819c	18	=head1 NAME
027d819c	19
5873cf38	20	Text::Tradition::StemmaUtil - standalone utilities for stemma graph display and
5873cf38	21	distance tree calculations
027d819c	22
	23	=head1 DESCRIPTION
	24
5873cf38	25	This package contains a set of utilities for displaying arbitrary stemmata and
5873cf38	26	running phylogenetic analysis on text collations.
027d819c	27
	28	=head1 SUBROUTINES
	29
5873cf38	30	=head2 display_graph( $graph, $opts )
	31
	32	Returns a dot specification intended for display, according to the logical
	33	attributes of the witnesses.
	34
	35	=cut
	36
	37	sub display_graph {
	38	my( $graph, $opts ) = @_;
	39
	40	# Get default and specified options
	41	my %graphopts = (
	42	# 'ratio' => 1,
	43	'bgcolor' => 'transparent',
	44	);
	45	my %nodeopts = (
	46	'fontsize' => 11,
	47	'style' => 'filled',
	48	'fillcolor' => 'white',
	49	'color' => 'white',
	50	'shape' => 'ellipse', # Shape for the extant nodes
	51	);
	52	my %edgeopts = (
	53	'arrowhead' => 'none',
	54	);
	55	@graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}}
	56	if $opts->{'graph'};
	57	@nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}}
	58	if $opts->{'node'};
	59	@edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}}
	60	if $opts->{'edge'};
	61
	62	my $gdecl = $graph->is_directed ? 'digraph' : 'graph';
	63	my $gname = $opts->{'name'} ? '"' . $opts->{'name'} . '"'
	64	: 'stemma';
	65	my @dotlines;
	66	push( @dotlines, "$gdecl $gname {" );
	67	## Print out the global attributes
	68	push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
	69	push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
	70	push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;
	71
	72	# Add each of the nodes.
	73	foreach my $n ( $graph->vertices ) {
	74	my %vattr = ( 'id' => $n ); # Set the SVG element ID to the sigil itself
	75	if( $graph->has_vertex_attribute( $n, 'label' ) ) {
	76	$vattr{'label'} = $graph->get_vertex_attribute( $n, 'label' );
	77	}
	78	push( @dotlines, _make_dotline( $n, %vattr ) );
	79	}
	80	# Add each of our edges.
	81	foreach my $e ( $graph->edges ) {
	82	my( $from, $to ) = map { _dotquote( $_ ) } @$e;
	83	my $connector = $graph->is_directed ? '->' : '--';
	84	push( @dotlines, " $from $connector $to;" );
	85	}
	86	push( @dotlines, '}' );
	87
	88	return join( "\n", @dotlines );
	89	}
	90
	91
	92	=head2 editable_graph( $graph, $opts )
	93
94	Returns a dot specification of a stemma graph with logical witness features,
95	intended for editing the stemma definition.
96
97	=cut
98
99	sub editable_graph {
100	my( $graph, $opts ) = @_;
101
102	# Create the graph
103	my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n";
104	my $fq = $opts->{'forcequote'};
105	my $gdecl = $graph->is_undirected ? 'graph' : 'digraph';
106	my $gname = exists $opts->{'name'} ? '"' . $opts->{'name'} . '"'
107	: 'stemma';
108	my @dotlines;
109	push( @dotlines, "$gdecl $gname {" );
110	my @real; # A cheap sort
111	foreach my $n ( sort $graph->vertices ) {
112	my $c = $graph->get_vertex_attribute( $n, 'class' );
113	$c = 'extant' unless $c;
114	if( $c eq 'extant' ) {
115	push( @real, $n );
116	} else {
117	push( @dotlines, _make_dotline( $n, 'class' => $c, 'forcequote' => $fq ) );
118	}
119	}
120	# Now do the real ones
121	foreach my $n ( @real ) {
122	push( @dotlines, _make_dotline( $n, 'class' => 'extant', 'forcequote' => $fq ) );
123	}
124	foreach my $e ( sort _by_vertex $graph->edges ) {
125	my( $from, $to ) = map { _dotquote( $_ ) } @$e;
126	my $conn = $graph->is_undirected ? '--' : '->';
127	push( @dotlines, " $from $conn $to;" );
128	}
129	push( @dotlines, '}' );
130	return join( $join, @dotlines );
131	}
132
133	sub _make_dotline {
134	my( $obj, %attr ) = @_;
135	my @pairs;
136	my $fq = delete $attr{forcequote};
137	foreach my $k ( keys %attr ) {
138	my $v = _dotquote( $attr{$k}, $fq );
139	push( @pairs, "$k=$v" );
140	}
141	return sprintf( " %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) );
142	}
143
144	sub _dotquote {
145	my( $str, $force ) = @_;
146	return $str if $str =~ /^[A-Za-z0-9]+$/;
147	$str =~ s/\"/\\\"/g;
148	$str = '"' . $str . '"';
149	return $str;
150	}
151
152	sub _by_vertex {
153	return $a->[0].$a->[1] cmp $b->[0].$b->[1];
154	}
155
ea45d2a6	156	=head2 character_input( $tradition, $opts )
9457207b	157
	158	Returns a character matrix string suitable for Phylip programs, which
	159	corresponds to the given alignment table. See Text::Tradition::Collation
ea45d2a6	160	for a description of the alignment table format. Options include:
	161
	162	=over
	163
	164	=item * exclude_layer - Exclude layered witnesses from the character input,
	165	using only the 'main' text of the witnesses in the tradition.
	166
	167	=item * collapse - A reference to an array of relationship names that should
	168	be treated as equivalent for the purposes of generating the character matrix.
	169
	170	=back
9457207b	171
027d819c	172	=cut
027d819c	173
9457207b	174	sub character_input {
ea45d2a6	175	my ( $tradition, $opts ) = @_;
	176	my $table = $tradition->collation->alignment_table;
	177	if( $opts->{exclude_layer} ) {
	178	# Filter out all alignment table rows that do not correspond
	179	# to a named witness - these are the layered witnesses.
b39e7cb5	180	my $newtable = { alignment => [], length => $table->{length} };
b39e7cb5	181	foreach my $row ( @{$table->{alignment}} ) {
ea45d2a6	182	if( $tradition->has_witness( $row->{witness} ) ) {
	183	push( @{$newtable->{alignment}}, $row );
	184	}
	185	}
	186	$table = $newtable;
	187	}
	188	my $character_matrix = _make_character_matrix( $table, $opts );
9457207b	189	my $input = '';
	190	my $rows = scalar @{$character_matrix};
	191	my $columns = scalar @{$character_matrix->[0]} - 1;
	192	$input .= "\t$rows\t$columns\n";
	193	foreach my $row ( @{$character_matrix} ) {
	194	$input .= join( '', @$row ) . "\n";
	195	}
	196	return $input;
	197	}
	198
027d819c	199	sub _make_character_matrix {
ea45d2a6	200	my( $table, $opts ) = @_;
68454b71	201	# Push the names of the witnesses to initialize the rows of the matrix.
	202	my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] }
	203	@{$table->{'alignment'}};
	204	foreach my $token_index ( 0 .. $table->{'length'} - 1) {
ea45d2a6	205	my @pos_tokens = map { $_->{'tokens'}->[$token_index] }
68454b71	206	@{$table->{'alignment'}};
ea45d2a6	207	my @pos_readings = map { $_ ? $_->{'t'} : $_ } @pos_tokens;
ea45d2a6	208	my @chars = _convert_characters( \@pos_readings, $opts );
68454b71	209	foreach my $idx ( 0 .. $#matrix ) {
	210	push( @{$matrix[$idx]}, $chars[$idx] );
	211	}
	212	}
	213	return \@matrix;
	214	}
	215
	216	# Helper function to make the witness name something legal for pars
	217
	218	sub _normalize_witname {
	219	my( $witname ) = @_;
	220	$witname =~ s/\s+/ /g;
	221	$witname =~ s/[\[\]\(\)\:;,]//g;
	222	$witname = substr( $witname, 0, 10 );
	223	return sprintf( "%-10s", $witname );
	224	}
	225
027d819c	226	sub _convert_characters {
ea45d2a6	227	my( $row, $opts ) = @_;
68454b71	228	# This is a simple algorithm that treats every reading as different.
	229	# Eventually we will want to be able to specify how relationships
	230	# affect the character matrix.
	231	my %unique = ( '__UNDEF__' => 'X',
	232	'#LACUNA#' => '?',
	233	);
ea45d2a6	234	my %equivalent;
68454b71	235	my %count;
68454b71	236	my $ctr = 0;
ea45d2a6	237	foreach my $rdg ( @$row ) {
	238	next unless $rdg;
	239	next if $rdg->is_lacuna;
	240	next if exists $unique{$rdg->text};
	241	if( ref( $opts->{'collapse'} ) eq 'ARRAY' ) {
	242	my @exclude_types = @{$opts->{'collapse'}};
	243	my @set = $rdg->related_readings( sub { my $rel = shift;
	244	$rel->colocated && grep { $rel->type eq $_ } @exclude_types } );
	245	push( @set, $rdg );
	246	my $char = chr( 65 + $ctr++ );
	247	map { $unique{$_->text} = $char } @set;
	248	$count{$rdg->text} += scalar @set;
	249	} else {
	250	$unique{$rdg->text} = chr( 65 + $ctr++ );
	251	$count{$rdg->text}++;
	252	}
68454b71	253	}
	254	# Try to keep variants under 8 by lacunizing any singletons.
	255	if( scalar( keys %unique ) > 8 ) {
	256	foreach my $word ( keys %count ) {
	257	if( $count{$word} == 1 ) {
	258	$unique{$word} = '?';
	259	}
	260	}
	261	}
	262	my %u = reverse %unique;
	263	if( scalar( keys %u ) > 8 ) {
	264	warn "Have more than 8 variants on this location; phylip will break";
	265	}
ea45d2a6	266	my @chars = map { $_ ? $unique{$_->text} : $unique{'__UNDEF__' } } @$row;
68454b71	267	return @chars;
	268	}
	269
027d819c	270	=head2 phylip_pars( $character_matrix )
	271
	272	Runs Phylip Pars on the given character matrix. Returns results in Newick format.
	273
	274	=cut
	275
b02332ca	276	sub phylip_pars {
	277	my( $charmatrix ) = @_;
	278	# Set up a temporary directory for all the default Phylip files.
	279	my $phylip_dir = File::Temp->newdir();
	280	# $phylip_dir->unlink_on_destroy(0);
	281	# We need an infile, and we need a command input file.
	282	open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
	283	print MATRIX $charmatrix;
	284	close MATRIX;
	285
	286	open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
	287	## TODO any configuration parameters we want to set here
	288	# U Search for best tree? Yes
	289	# S Search option? More thorough search
	290	# V Number of trees to save? 100
	291	# J Randomize input order of species? No. Use input order
	292	# O Outgroup root? No, use as outgroup species 1
	293	# T Use Threshold parsimony? No, use ordinary parsimony
	294	# W Sites weighted? No
	295	# M Analyze multiple data sets? No
	296	# I Input species interleaved? Yes
	297	# 0 Terminal type (IBM PC, ANSI, none)? ANSI
	298	# 1 Print out the data at start of run No
	299	# 2 Print indications of progress of run Yes
	300	# 3 Print out tree Yes
	301	# 4 Print out steps in each site No
	302	# 5 Print character at all nodes of tree No
	303	# 6 Write out trees onto tree file? Yes
	304	print CMD "Y\n";
	305	close CMD;
	306
	307	# And then we run the program.
	308	my $program = File::Which::which( 'pars' );
b39e7cb5	309	unless( $program && -x $program ) {
edac47cc	310	throw( "Phylip pars not found in path" );
b02332ca	311	}
	312
	313	{
	314	# We need to run it in our temporary directory where we have created
	315	# all the expected files.
	316	local $CWD = $phylip_dir;
	317	my @cmd = ( $program );
	318	run \@cmd, '<', 'cmdfile', '>', '/dev/null';
	319	}
	320	# Now our output should be in 'outfile' and our tree in 'outtree',
	321	# both in the temp directory.
	322
	323	my @outtree;
	324	if( -f "$phylip_dir/outtree" ) {
	325	open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
	326	@outtree = <TREE>;
	327	close TREE;
	328	}
edac47cc	329	return join( '', @outtree ) if @outtree;
b02332ca	330
69403daa	331	# If we got this far, we are about to throw an error.
b02332ca	332	my @error;
	333	if( -f "$phylip_dir/outfile" ) {
	334	open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read";
	335	@error = <OUTPUT>;
	336	close OUTPUT;
	337	} else {
	338	push( @error, "Neither outtree nor output file was produced!" );
	339	}
edac47cc	340	throw( join( '', @error ) );
b02332ca	341	}
b02332ca	342
027d819c	343	=head2 parse_newick( $newick_string )
027d819c	344
ea45d2a6	345	Parses the given Newick tree(s) into one or more Stemma objects with
ea45d2a6	346	undirected graphs.
027d819c	347
	348	=cut
	349
b02332ca	350	sub parse_newick {
b02332ca	351	my $newick = shift;
5873cf38	352	# Parse the result into a set of trees and return them.
b02332ca	353	my $forest = Bio::Phylo::IO->parse(
	354	-format => 'newick',
	355	-string => $newick,
	356	);
5873cf38	357	return map { _graph_from_bio( $_ ) } @{$forest->get_entities};
ea45d2a6	358	}
	359
	360	sub _graph_from_bio {
	361	my $tree = shift;
	362	my $graph = Graph->new( 'undirected' => 1 );
	363	# Give all the intermediate anonymous nodes a name.
	364	my $i = 0;
	365	my $classes = {};
	366	foreach my $n ( @{$tree->get_terminals} ) {
	367	# The terminal nodes are our named witnesses.
	368	$classes->{$n->get_name} = 'extant';
	369	}
	370	foreach my $n ( @{$tree->get_internals} ) {
	371	unless( defined $n->get_name && $n->get_name ne '' ) {
	372	# Get an integer, make sure it's a unique name
	373	while( exists $classes->{$i} ) {
	374	$i++;
	375	}
	376	$n->set_name( $i++ );
	377	}
	378	$classes->{$n->get_name} = 'hypothetical';
	379	}
	380	_add_tree_children( $graph, $classes, undef, [ $tree->get_root ]);
	381	return $graph;
	382	}
	383
	384	sub _add_tree_children {
	385	my( $graph, $classes, $parent, $tree_children ) = @_;
	386	foreach my $c ( @$tree_children ) {
	387	my $child = $c->get_name;
	388	$graph->add_vertex( $child );
	389	$graph->set_vertex_attribute( $child, 'class', $classes->{$child} );
	390	$graph->add_path( $parent, $child ) if defined $parent;
	391	_add_tree_children( $graph, $classes, $child, $c->get_children() );
b02332ca	392	}
b02332ca	393	}
b02332ca	394
027d819c	395	=head2 newick_to_svg( $newick_string )
	396
	397	Uses the FigTree utility (if installed) to transform the given Newick tree(s)
	398	into a graph visualization.
	399
	400	=cut
	401
27e2a8fe	402	sub newick_to_svg {
	403	my $newick = shift;
	404	my $program = File::Which::which( 'figtree' );
	405	unless( -x $program ) {
edac47cc	406	throw( "FigTree commandline utility not found in path" );
27e2a8fe	407	}
	408	my $svg;
	409	my $nfile = File::Temp->new();
	410	print $nfile $newick;
	411	close $nfile;
	412	my @cmd = ( $program, '-graphic', 'SVG', $nfile );
	413	run( \@cmd, ">", binary(), \$svg );
	414	return decode_utf8( $svg );
	415	}
	416
edac47cc	417	sub throw {
	418	Text::Tradition::Error->throw(
	419	'ident' => 'StemmaUtil error',
	420	'message' => $_[0],
	421	);
	422	}
	423
027d819c	424	1;
	425
	426	=head1 LICENSE
	427
	428	This package is free software and is provided "as is" without express
	429	or implied warranty. You can redistribute it and/or modify it under
	430	the same terms as Perl itself.
	431
	432	=head1 AUTHOR
	433
	434	Tara L Andrews E<lt>aurum@cpan.orgE<gt>