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# Copyright (c) 1997-2024
# Ewgenij Gawrilow, Michael Joswig, and the polymake team
# Technische Universität Berlin, Germany
# https://polymake.org
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any
# later version: http://www.gnu.org/licenses/gpl.txt.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#-------------------------------------------------------------------------------
# @category Visualization
# Attributes modifying the appearance of phylogenetic trees
options %Visual::PhylogeneticTree::decorations = (
%Visual::Graph::decorations,
);
object PhylogeneticTree {
user_method VISUAL(%Visual::PhylogeneticTree::decorations) {
my ($this, $decor)=@_;
my $coord = $this->tree_embedding;
visualize( new Visual::PhylogeneticTree( Name => $this->name,
Graph => $this,
Coord => $coord,
NodeLabels => $this->LABELS,
EdgeLabels => $this->EDGE_LENGTHS,
$decor,
));
}
sub tree_embedding {
my ($this)=@_;
my $n_leaves = $this->N_TAXA;
my $adj = $this->ADJACENCY;
my $el = $this->EDGE_LENGTHS;
my $leaf_counter = 0;
my @positions;
$positions[0] = new Vector(0, $n_leaves/2);
foreach (@{$adj->adjacent_nodes(0)}) {
calc_pos_recursive($_, 0);
}
return convert_to<Float>(new Matrix(@positions));
sub calc_pos_recursive {
my ($current_node, $pred) = @_;
# the y coordinate is later changed after it has been computed for the nodes in the succeeding subtree
$positions[$current_node] = new Vector($positions[$pred]->[0] + $el->[$adj->edge($current_node, $pred)], 0);
my $n_adj_nodes = $adj->adjacent_nodes($current_node)->size;
if ($n_adj_nodes == 1) {
# its a leaf
$positions[$current_node]->[1] = $leaf_counter;
$leaf_counter++;
} else {
my $succ_y = 0;
foreach (@{$adj->adjacent_nodes($current_node)}) {
next if ($_ == $pred);
calc_pos_recursive($_, $current_node);
$succ_y += $positions[$_]->[1];
}
$positions[$current_node]->[1] = $succ_y/($n_adj_nodes-1);
}
}
}
}
# Local Variables:
# mode: perl
# cperl-indent-level:3
# indent-tabs-mode:nil
# End:
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