From 82e7472ab8dc0e84c1d5b43aff03af67f33e799f Mon Sep 17 00:00:00 2001 From: theosanderson Date: Sat, 10 Jul 2021 14:44:47 +0100 Subject: [PATCH] updates --- src/helpers/tree.js | 34 +++++++++++++++------------------- 1 file changed, 15 insertions(+), 19 deletions(-) diff --git a/src/helpers/tree.js b/src/helpers/tree.js index 7b99ffc1..890d6343 100644 --- a/src/helpers/tree.js +++ b/src/helpers/tree.js @@ -1,6 +1,5 @@ /* eslint-disable */ -window.newick = 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- +window.newick="((A:1,EE:5):3,B:2,(C:5,D:2):3)" function kn_parse(str) { var stack = new Array(); var tree = new Object(); @@ -52,7 +51,7 @@ function kn_add_node(str, l, tree, x) // private method { var r, beg, end = 0, z; - for (i = l, beg = l; i < str.length && str.charAt(i) != ',' && str.charAt(i) != ')'; ++i) { + for (var i = l, beg = l; i < str.length && str.charAt(i) != ',' && str.charAt(i) != ')'; ++i) { var c = str.charAt(i); if (c == '[') { var meta_beg = i; @@ -70,12 +69,12 @@ function kn_add_node(str, l, tree, x) // private method if ((cc < '0' || cc > '9') && cc != 'e' && cc != 'E' && cc != '+' && cc != '-' && cc != '.') break; } - distance = parseFloat(str.substr(j, i - j)); + var distance = parseFloat(str.substr(j, i - j)); --i; } else if (c < '!' && c > '~' && end == 0) end = i; } if (end == 0) end = i; - node_name = "" + var node_name = "" if (end > beg) node_name = str.substr(beg, end - beg); tree.names.push(node_name); tree.distances.push(distance) @@ -147,18 +146,17 @@ function kn_expand_node(tree, root) { function kn_reorder(tree, root) { - depths = {} - tip_numbers = {} - weights = {} - window.weights=weights - window.tip_numbers =tip_numbers - sort_leaf = function (a, b) { + var depths = {} + var tip_numbers = {} + var weights = {} + + var sort_leaf = function (a, b) { if (depths[a] < depths[b]) return 1; if (depths[a] > depths[b]) return -1; return String(tree.names[a]) < String(tree.names[b]) ? -1 : String(tree.names[a]) > String(tree.names[b]) ? 1 : 0; }; - sort_weight = function (a, b) { return weights[a] / tip_numbers[a] - weights[b] / tip_numbers[b]; }; - console.log("yp") + var sort_weight = function (a, b) { return weights[a] / tip_numbers[a] - weights[b] / tip_numbers[b]; }; + //console.log("yp") var x = new Array(); var i, node = kn_expand_node(tree,root); window.node= node @@ -188,12 +186,10 @@ function kn_reorder(tree, root) { for (i = 0; i < node.length; ++i) if (tree.children[node[i]].length >= 2) tree.children[node[i]].sort(sort_weight); - console.log("node",node) - console.log("weight",weights) + //console.log("node",node) + // console.log("weight",weights) } -window.kn_expand_node = kn_expand_node -window.kn_reorder = kn_reorder -window.kn_parse = kn_parse; -window.kn_calxy = kn_calxy + +export {kn_expand_node,kn_reorder,kn_parse,kn_calxy}