diff options
Diffstat (limited to 'Master/texmf-dist/tex/generic/pgf/graphdrawing/lua/pgf/gd/phylogenetics/PhylogeneticTree.lua')
-rw-r--r-- | Master/texmf-dist/tex/generic/pgf/graphdrawing/lua/pgf/gd/phylogenetics/PhylogeneticTree.lua | 46 |
1 files changed, 23 insertions, 23 deletions
diff --git a/Master/texmf-dist/tex/generic/pgf/graphdrawing/lua/pgf/gd/phylogenetics/PhylogeneticTree.lua b/Master/texmf-dist/tex/generic/pgf/graphdrawing/lua/pgf/gd/phylogenetics/PhylogeneticTree.lua index f66f2553306..242ccf183ff 100644 --- a/Master/texmf-dist/tex/generic/pgf/graphdrawing/lua/pgf/gd/phylogenetics/PhylogeneticTree.lua +++ b/Master/texmf-dist/tex/generic/pgf/graphdrawing/lua/pgf/gd/phylogenetics/PhylogeneticTree.lua @@ -29,53 +29,53 @@ local declare = InterfaceToAlgorithms.declare declare { key = "phylogenetic tree layout", algorithm = PhylogeneticTree, - + postconditions = { upward_oriented = true }, - summary = [[" - Layout for drawing phylogenetic trees. + 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 }; + \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 +-- "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 + -- 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 { |