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 Moose;
-use Text::Tradition::Collation::Position;
use Graph;
+use Graph::Convert;
use Graph::Reader::Dot;
+use IPC::Run qw/ run binary /;
+use Moose;
+use Text::Balanced qw/ extract_bracketed /;
has collation => (
is => 'ro',
required => 1,
);
-has character_matrix => (
- is => 'ro',
- isa => 'ArrayRef[ArrayRef[Str]]',
- writer => '_save_character_matrix',
- predicate => 'has_character_matrix',
- );
-
+# TODO Think about making a new class for the graphs, which has apsp as a property.
has graph => (
is => 'rw',
isa => 'Graph',
);
has apsp => (
- is => 'rw',
+ is => 'ro',
isa => 'Graph',
+ writer => '_save_apsp',
+ );
+
+has distance_trees => (
+ is => 'ro',
+ isa => 'ArrayRef[Graph]',
+ writer => '_save_distance_trees',
+ predicate => 'has_distance_trees',
+ );
+
+has distance_apsps => (
+ is => 'ro',
+ isa => 'ArrayRef[Graph]',
+ writer => '_save_distance_apsps',
);
sub BUILD {
my( $self, $args ) = @_;
# If we have been handed a dotfile, initialize it into a graph.
if( exists $args->{'dot'} ) {
+ # Open the file, assume UTF-8
+ open( my $dot, $args->{'dot'} ) or warn "Failed to read dot file";
+ # TODO don't bother if we haven't opened
+ binmode $dot, ":utf8";
my $reader = Graph::Reader::Dot->new();
- my $graph = $reader->read_graph( $args->{'dot'} );
+ my $graph = $reader->read_graph( $dot );
$graph
? $self->graph( $graph )
: warn "Failed to parse dot file " . $args->{'dot'};
}
-
- # If we have a graph, calculate all the shortest paths between nodes,
- # disregarding direction.
- if( $self->has_graph ) {
+}
+
+# If we are saving a new graph, calculate its apsp values.
+after 'graph' => sub {
+ my( $self, $args ) = @_;
+ if( $args ) {
+ # We had a new graph.
my $undirected;
if( $self->graph->is_directed ) {
# Make an undirected version.
} else {
$undirected = $self->graph;
}
- $self->apsp( $undirected->APSP_Floyd_Warshall() );
+ $self->_save_apsp( $undirected->APSP_Floyd_Warshall() );
+ }
+};
+
+# Render the stemma as SVG.
+sub as_svg {
+ my( $self, $opts ) = @_;
+ # TODO add options for display, someday
+ my $dgraph = Graph::Convert->as_graph_easy( $self->graph );
+ # Set some class display attributes for 'hypothetical' and 'extant' nodes
+ $dgraph->set_attribute( 'flow', 'south' );
+ foreach my $n ( $dgraph->nodes ) {
+ if( $n->attribute( 'class' ) eq 'hypothetical' ) {
+ $n->set_attribute( 'shape', 'point' );
+ $n->set_attribute( 'pointshape', 'diamond' );
+ } else {
+ $n->set_attribute( 'shape', 'ellipse' );
+ }
}
+
+ # Render to svg via graphviz
+ my @lines = split( /\n/, $dgraph->as_graphviz() );
+ # Add the size attribute
+ if( $opts->{'size'} ) {
+ my $sizeline = " graph [ size=\"" . $opts->{'size'} . "\" ]";
+ splice( @lines, 1, 0, $sizeline );
+ }
+ 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 join( "\n", @lines );
+ push( @cmd, $dotfile->filename );
+ run( \@cmd, ">", binary(), \$svg );
+ $svg = decode_utf8( $svg );
+ return $svg;
}
-
+
+#### 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 );
+ # and calculate their APSP values.
+ my @apsps;
+ foreach my $t ( @$trees ) {
+ push( @apsps, $t->APSP_Floyd_Warshall() );
+ }
+ $self->_save_distance_apsps( \@apsps );
+ } else {
+ warn "Failed to calculate distance trees: $result";
+ }
+ }
+};
sub make_character_matrix {
my $self = shift;
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]};
- $DB::single = 1;
foreach my $token_index ( 1 .. $#{$table} ) {
# First implementation: make dumb alignment table, caring about
# nothing except which reading is in which position.
push( @{$matrix[$idx]}, $chars[$idx] );
}
}
- $self->_save_character_matrix( \@matrix );
+ return \@matrix;
}
sub _normalize_ac {
}
}
if( scalar( keys %unique ) > 8 ) {
- warn "Have more than 8 variants on this location; pars will break";
+ 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();
- print STDERR $phylip_dir . "\n";
# $phylip_dir->unlink_on_destroy(0);
# We need an infile, and we need a command input file.
open( MATRIX, ">$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";
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;
projects / scpubgit/stemmatology.git / blobdiff