Dynamic bp tree

empress/support_files/js/bp-tree.js

@@ -65,7 +65,7 @@ define(["ByteArray", "underscore"], function (ByteArray, _) {
  /**
  * @type {Array}
  * @private
- * stores the name of each node in preorder. If names are not provided
+ * stores the name of each node in postorder. If names are not provided
  * then the names will be set to null by default.
  * Note: if memory becomes an issue this could be converted into a
  * Uint16Array
@@ -85,7 +85,7 @@ define(["ByteArray", "underscore"], function (ByteArray, _) {
  /**
  * @type {Array}
  * @private
- * Stores the length of the nodes in preorder. If lengths are not
+ * Stores the length of the nodes in postorder. If lengths are not
  * provided then lengths will be set to null.
  */
  this.lengths_ = lengths ? lengths : null;
@@ -971,5 +971,64 @@ define(["ByteArray", "underscore"], function (ByteArray, _) {
  return this._nameToNodes[name];
  };
 
+ /**
+ * tips - Set
+ */
+ BPTree.prototype.shear = function (keepTips) {
+ // closure
+ var scope = this;
+
+ // create new names and lengths array
+ var names = [null];
+ var lengths = [null];
+
+ // create new bit array
+ var mask = [];
+
+ // function to that will set open/close bits for a node
+ var set_bits = (node) => {
+ mask[node] = 1;
+ mask[scope.close(node)] = 0;
+ };
+
+ // set root open/close bits
+ set_bits(this.root());
+
+ // iterate over bp tree in post order and add all tips that are in
+ // keepTips plus their ancestors
+ var i;
+ for (i = 1; i <= this.size; i++) {
+ var node = this.postorderselect(i);
+ var name = this.name(node);
+ if (this.isleaf(node) && keepTips.has(name)) {
+ // set open/close bits for tip
+ set_bits(node);
+
+ // set open/close bits for tips ancestors
+ var parent = this.parent(node);
+ while (parent !== this.root() || mask[parent] !== 1) {
+ set_bits(parent);
+ parent = this.parent(parent);
+ }
+ }
+ }
+
+ var newBitArray = [];
+ for (i = 0; i < mask.length; i++) {
+ if (mask[i] !== undefined) {
+ newBitArray.push(mask[i]);
+ }
+
+ // get name and length of node
+ // Note: names and lengths of nodes are stored in postorder
+
+ if (mask[i] === 0) {
+ names.push(this.name(i));
+ lengths.push(this.length(i));
+ }
+ }
+ return new BPTree(newBitArray, names, lengths, null);
+ };
+
  return BPTree;
 });

tests/test-bp-tree.js

@@ -877,5 +877,101 @@ require(["jquery", "ByteArray", "BPTree"], function ($, ByteArray, BPTree) {
  "Error thrown when no length info given"
  );
  });
+
+ test("Test shear", function () {
+ // test modified from https://github.com/wasade/improved-octo-waddle/blob/master/bp/tests/test_bp.py#L228
+ // newick represenation
+ // ((3,4,(6)5)2, 7, ((10, 11)9)8)r;
+ var preShearArr = [
+ 1,
+ 1,
+ 1,
+ 0,
+ 1,
+ 0,
+ 1,
+ 1,
+ 0,
+ 0,
+ 0,
+ 1,
+ 0,
+ 1,
+ 1,
+ 1,
+ 0,
+ 1,
+ 0,
+ 0,
+ 0,
+ 0,
+ ];
+ var preShearNames = [
+ null,
+ "3",
+ "4",
+ "6",
+ "5",
+ "2",
+ "7",
+ "10",
+ "11",
+ "9",
+ "8",
+ "r",
+ ];
+ var preShearLenghts = [null, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11];
+ var preShearBPTree = new BPTree(
+ preShearArr,
+ preShearNames,
+ preShearLenghts,
+ null
+ );
+
+ var keep = new Set(["4", "6", "7", "10", "11"]);
+ var result = preShearBPTree.shear(keep);
+ deepEqual(result.b_, [
+ 1,
+ 1,
+ 1,
+ 0,
+ 1,
+ 1,
+ 0,
+ 0,
+ 0,
+ 1,
+ 0,
+ 1,
+ 1,
+ 1,
+ 0,
+ 1,
+ 0,
+ 0,
+ 0,
+ 0,
+ ]);
+ deepEqual(result.names_, [
+ null,
+ "4",
+ "6",
+ "5",
+ "2",
+ "7",
+ "10",
+ "11",
+ "9",
+ "8",
+ "r",
+ ]);
+ deepEqual(result.lengths_, [null, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]);
+
+ keep = new Set(["7", "10", "11"]);
+ result = preShearBPTree.shear(keep);
+ deepEqual(result.b_, [1, 1, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0]);
+ deepEqual(result.names_, [null, "7", "10", "11", "9", "8", "r"]);
+ deepEqual(result.lengths_, [null, 6, 7, 8, 9, 10, 11]);
+ });
  });
 });