package Text::Tradition::Stemma;
+use Bio::Phylo::IO;
+use Encode qw( decode_utf8 );
use File::chdir;
use File::Temp;
-use IPC::Run qw/ run /;
+use Graph;
+use Graph::Reader::Dot;
+use IPC::Run qw/ run binary /;
use Moose;
-use Text::Tradition::Collation::Position;
has collation => (
is => 'ro',
isa => 'Text::Tradition::Collation',
required => 1,
+ weak_ref => 1,
);
-has character_matrix => (
+has graph => (
+ is => 'rw',
+ isa => 'Graph',
+ predicate => 'has_graph',
+ );
+
+has distance_trees => (
is => 'ro',
- isa => 'ArrayRef[ArrayRef[Str]]',
- writer => '_save_character_matrix',
- predicate => 'has_character_matrix',
+ 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 @all_pos = sort { Text::Tradition::Collation::Position::str_cmp( $a, $b ) }
- $self->collation->possible_positions;
- my $table = [];
- my $characters = {};
- map { $characters->{$_} = {} } @all_pos;
- foreach my $wit ( @{$self->collation->tradition->witnesses} ) {
- # First implementation: make dumb alignment table, caring about
- # nothing except which reading is in which position.
- my $sigilfield = sprintf( "%-10s", $wit->sigil );
- push( @$table, [ $sigilfield, make_witness_row( $characters, $wit->path,
- \@all_pos ) ] );
- if( $wit->has_ante_corr ) {
- $sigilfield = sprintf( "%-10s", $wit->sigil . "_ac" );
- push( @$table, [ $sigilfield,
- make_witness_row( $characters, $wit->uncorrected_path,
- \@all_pos ) ] );
- }
- }
- $self->_save_character_matrix( $table );
-}
+ 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 make_witness_row {
- my( $characters, $path, $positions ) = @_;
- my %char_hash;
- map { $char_hash{$_} = 'X' } @$positions;
- foreach my $rdg( @$path ) {
- $char_hash{$rdg->position->minref} = get_character( $rdg, $characters );
+sub _normalize_ac {
+ my( $self, $witname ) = @_;
+ my $ac = $self->collation->ac_label;
+ if( $witname =~ /(.*)\Q$ac\E$/ ) {
+ $witname = $1 . '_ac';
}
- my @row = map { $char_hash{$_} } @$positions;
- return @row;
+ return sprintf( "%-10s", $witname );
}
-
-sub get_character {
- my( $reading, $characters ) = @_;
- my $this_pos = $characters->{$reading->position->minref};
+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 $text = $reading->text;
- unless( exists $this_pos->{$text} ) {
- # We need to find what the next character is here, and record it.
- my @all_chr = sort { $a <=> $b } values( %$this_pos );
- if( @all_chr == 8 ) {
- warn "Already have eight variants at position "
- . $reading->position->minref . "; not adding " . $reading->text;
- return '?';
- }
- $this_pos->{$text} = scalar @all_chr;
+ 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;
}
- return $this_pos->{$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 { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
+ return @chars;
}
-sub pars_input {
+sub phylip_pars_input {
my $self = shift;
- $self->make_character_matrix unless $self->has_character_matrix;
- my $matrix = '';
- my $rows = scalar @{$self->character_matrix};
- my $columns = scalar @{$self->character_matrix->[0]} - 1;
- $matrix .= "\t$rows\t$columns\n";
- foreach my $row ( @{$self->character_matrix} ) {
- $matrix .= join( '', @$row ) . "\n";
- }
- return $matrix;
+ 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_pars {
+sub run_phylip_pars {
my $self = shift;
# Set up a temporary directory for all the default Phylip files.
my $phylip_dir = File::Temp->newdir();
- $DB::single = 1;
+ # $phylip_dir->unlink_on_destroy(0);
# We need an infile, and we need a command input file.
open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
- print MATRIX $self->pars_input();
+ print MATRIX $self->phylip_pars_input();
close MATRIX;
open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
my $PHYLIP_PATH = '/Users/tla/Projects/phylip-3.69/exe';
my $program = "pars";
if( $^O eq 'darwin' ) {
- $program = "$PHYLIP_PATH/$program.app/Contents/MacOS/$program";
+ $program = "$PHYLIP_PATH/$program.app/Contents/MacOS/$program";
} else {
- $program = "$PHYLIP_PATH/$program";
+ $program = "$PHYLIP_PATH/$program";
}
{
- # 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';
+ # 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, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
- @outtree = <TREE>;
- close TREE;
+ open( TREE, "$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;
+ 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!" );
+ 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;