package Text::Tradition::Stemma;
use Bio::Phylo::IO;
+use Encode qw( decode_utf8 );
use File::chdir;
use File::Temp;
use Graph;
+use Graph::Convert;
use Graph::Reader::Dot;
-use IPC::Run qw/ run /;
+use IPC::Run qw/ run binary /;
use Moose;
use Text::Balanced qw/ extract_bracketed /;
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 => (
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 = shift;
+ # 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 @cmd = qw/dot -Tsvg/;
+ my( $svg, $err );
+ my $dotfile = File::Temp->new();
+ ## TODO REMOVE
+ # $dotfile->unlink_on_destroy(0);
+ binmode $dotfile, ':utf8';
+ print $dotfile $dgraph->as_graphviz();
+ 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 = @_;
# We need to make a tree before we can return it.
my( $ok, $result ) = $self->run_phylip_pars();
if( $ok ) {
- $self->_save_distance_trees( _parse_newick( $result ) );
+ # 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 tree: $result";
+ warn "Failed to calculate distance trees: $result";
}
}
};
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 {
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";
+ 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 $matrix;
+ return $input;
}
sub run_phylip_pars {