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-- Copyright 2013 by Sarah Mäusle and Till Tantau
--
-- This file may be distributed an/or modified
--
-- 1. under the LaTeX Project Public License and/or
-- 2. under the GNU Public License
--
-- See the file doc/generic/pgf/licenses/LICENSE for more information
-- @release $Header$
local PhylogeneticTree = {}
-- Namespace
require("pgf.gd.phylogenetics").PhylogeneticTree = PhylogeneticTree
-- Imports
local InterfaceToAlgorithms = require "pgf.gd.interface.InterfaceToAlgorithms"
local Storage = require "pgf.gd.lib.Storage"
local Direct = require "pgf.gd.lib.Direct"
-- Shorthand:
local declare = InterfaceToAlgorithms.declare
---
declare {
key = "phylogenetic tree layout",
algorithm = PhylogeneticTree,
postconditions = {
upward_oriented = true
},
summary = [["
Layout for drawing phylogenetic trees.
"]],
documentation = [["
...
"]],
examples = [["
\tikz \graph [phylogenetic tree layout, upgma,
distance matrix={
0 4 9 9 9 9 9
4 0 9 9 9 9 9
9 9 0 2 7 7 7
9 9 2 0 7 7 7
9 9 7 7 0 3 5
9 9 7 7 3 0 5
9 9 7 7 5 5 0}]
{ a, b, c, d, e, f, g };
"]]
}
-- Computes a phylogenetic tree and/or visualizes it
-- - computes a phylogenetic tree according to what the "phylogenetic
-- algorithm" key is set to
-- - invokes a graph drawing algorithm according to what the
-- "phylogenetic layout" key is set to
function PhylogeneticTree:run()
local options = self.digraph.options
-- Two storages for some information computed by the phylogenetic
-- tree generation algorithm
local lengths = Storage.newTableStorage()
-- First, compute the phylogenetic tree
local tree = options.algorithm_phases['phylogenetic tree generation'].new {
main_algorithm = self,
lengths = lengths
}:run()
tree = Direct.ugraphFromDigraph(tree)
-- Second, layout the tree
local layout_class = options.algorithm_phases['phylogenetic tree layout']
layout_class.new {
main_algorithm = self,
distances = distances,
lengths = lengths,
tree = tree
}:run()
tree:sync()
end
return PhylogeneticTree
|