/**
 * Newick format parser in JavaScript.
 *
 * Copyright (c) Jason Davies 2010.
 *  
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *  
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *  
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 *
 * Example tree (from http://en.wikipedia.org/wiki/Newick_format):
 *
 * +--0.1--A
 * F-----0.2-----B            +-------0.3----C
 * +------------------0.5-----E
 *                            +---------0.4------D
 *
 * Newick format:
 * (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
 *
 * Converted to JSON:
 * {
 *   name: "F",
 *   branchset: [
 *     {name: "A", length: 0.1},
 *     {name: "B", length: 0.2},
 *     {
 *       name: "E",
 *       length: 0.5,
 *       branchset: [
 *         {name: "C", length: 0.3},
 *         {name: "D", length: 0.4}
 *       ]
 *     }
 *   ]
 * }
 *
 * Converted to JSON, but with no names or lengths:
 * {
 *   branchset: [
 *     {}, {}, {
 *       branchset: [{}, {}]
 *     }
 *   ]
 * }
 */


// We at IBViz have made minor changes to this code. 

(function(exports) {
  exports.parse = function(s) {
      // added by Zach Sailer
      var iterate_name = 1
      //
    var ancestors = [];
    var tree = {};
    var tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
    for (var i=0; i<tokens.length; i++) {
      var token = tokens[i];
      switch (token) {
        case '(': // new branchset
          var subtree = {};
          tree.children = [subtree];
          ancestors.push(tree);
          tree = subtree;
          break;
        case ',': // another branch
          var subtree = {};
          ancestors[ancestors.length-1].children.push(subtree);
          tree = subtree;
          break;
        case ')': // optional name next
          tree = ancestors.pop();
          break;
        case ':': // optional length next
          break;
        default:
          var x = tokens[i-1];
          if (x == ')' || x == '(' || x == ',') {
              // added by Zach Sailer
              if (typeof token != "string" || token == ""){
                  tree.name = "split" + String(iterate_name);
                  iterate_name += 1
              } else {
                  tree.name = token;
              }
              //
          } else if (x == ':') {
            tree.size = parseFloat(token);
          }
      }
    }
    return tree;
  };
})(
    // exports will be set in any commonjs platform; use it if it's available
    typeof exports !== "undefined" ?
    exports :
    // otherwise construct a name space.  outside the anonymous function,
    // "this" will always be "window" in a browser, even in strict mode.
    this.Newick = {}
);
