alignment.js/helpers/jointSort.js

A suite of reusable [React](http://reactjs.org/) components for creating a variety of visualizations involving [multiple sequence alignments](https://en.wikipedia.org/wiki/Multiple_sequence_alignment). [View the live demo here](http://alignment.hyphy.org/

"use strict";

Object.defineProperty(exports, "__esModule", {
  value: true
});
exports["default"] = void 0;

var _d = require("d3");

function sortFASTAAndNewick(sequence_data, tree, strict) {
  var i = 0;
  tree.traverse_and_compute(function (n) {
    var d = 1;

    if (!n.name) {
      n.name = "Node" + i++;
    }

    if (n.children && n.children.length) {
      d += (0, _d.max)(n.children, function (d) {
        return d["count_depth"];
      });
    }

    n["count_depth"] = d;
  });
  tree.resortChildren(function (a, b) {
    return a["count_depth"] - b["count_depth"];
  });
  var ordered_leaf_names = tree.getTips().map(function (d) {
    return d.data.name;
  });
  sequence_data.sort(function (a, b) {
    var a_index = ordered_leaf_names.indexOf(a.header),
        b_index = ordered_leaf_names.indexOf(b.header);
    return a_index - b_index;
  });

  if (strict) {
    var number_of_leaves = ordered_leaf_names.length,
        lengths_agree = number_of_leaves == sequence_data.length;

    if (!lengths_agree) {
      throw "Different number of leaves and sequences!";
    }

    sequence_data.forEach(function (record, index) {
      var leaf = ordered_leaf_names[index],
          header = record.header;

      if (leaf != header) {
        throw "Tree/alignment mismatch at ".concat(i, ": ").concat(leaf, "/").concat(header, ".");
      }
    });
  }

  return tree;
}

var _default = sortFASTAAndNewick;
exports["default"] = _default;