"use strict";

exports.__esModule = true;
exports["default"] = exports.AlignmentToolDialog = void 0;
var _react = _interopRequireDefault(require("react"));
var _core = require("@blueprintjs/core");
var _teselagenReactComponents = require("teselagen-react-components");
var _reduxForm = require("redux-form");
var _bioParsers = require("@teselagen/bio-parsers");
var _lodash = require("lodash");
var _shortid = _interopRequireDefault(require("shortid"));
var _classnames = _interopRequireDefault(require("classnames"));
var _ToolbarItem = _interopRequireDefault(require("./ToolbarItem"));
var _withEditorProps = _interopRequireWildcard(require("../withEditorProps"));
var _GlobalDialogUtils = require("../GlobalDialogUtils");
var _recompose = require("recompose");
var _array_move = require("./array_move");
function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || typeof obj !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
function _regeneratorRuntime() { "use strict"; /*! regenerator-runtime -- Copyright (c) 2014-present, Facebook, Inc. -- license (MIT): https://github.com/facebook/regenerator/blob/main/LICENSE */ _regeneratorRuntime = function _regeneratorRuntime() { return exports; }; var exports = {}, Op = Object.prototype, hasOwn = Op.hasOwnProperty, defineProperty = Object.defineProperty || function (obj, key, desc) { obj[key] = desc.value; }, $Symbol = "function" == typeof Symbol ? Symbol : {}, iteratorSymbol = $Symbol.iterator || "@@iterator", asyncIteratorSymbol = $Symbol.asyncIterator || "@@asyncIterator", toStringTagSymbol = $Symbol.toStringTag || "@@toStringTag"; function define(obj, key, value) { return Object.defineProperty(obj, key, { value: value, enumerable: !0, configurable: !0, writable: !0 }), obj[key]; } try { define({}, ""); } catch (err) { define = function define(obj, key, value) { return obj[key] = value; }; } function wrap(innerFn, outerFn, self, tryLocsList) { var protoGenerator = outerFn && outerFn.prototype instanceof Generator ? outerFn : Generator, generator = Object.create(protoGenerator.prototype), context = new Context(tryLocsList || []); return defineProperty(generator, "_invoke", { value: makeInvokeMethod(innerFn, self, context) }), generator; } function tryCatch(fn, obj, arg) { try { return { type: "normal", arg: fn.call(obj, arg) }; } catch (err) { return { type: "throw", arg: err }; } } exports.wrap = wrap; var ContinueSentinel = {}; function Generator() {} function GeneratorFunction() {} function GeneratorFunctionPrototype() {} var IteratorPrototype = {}; define(IteratorPrototype, iteratorSymbol, function () { return this; }); var getProto = Object.getPrototypeOf, NativeIteratorPrototype = getProto && getProto(getProto(values([]))); NativeIteratorPrototype && NativeIteratorPrototype !== Op && hasOwn.call(NativeIteratorPrototype, iteratorSymbol) && (IteratorPrototype = NativeIteratorPrototype); var Gp = GeneratorFunctionPrototype.prototype = Generator.prototype = Object.create(IteratorPrototype); function defineIteratorMethods(prototype) { ["next", "throw", "return"].forEach(function (method) { define(prototype, method, function (arg) { return this._invoke(method, arg); }); }); } function AsyncIterator(generator, PromiseImpl) { function invoke(method, arg, resolve, reject) { var record = tryCatch(generator[method], generator, arg); if ("throw" !== record.type) { var result = record.arg, value = result.value; return value && "object" == typeof value && hasOwn.call(value, "__await") ? 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"completed" : "suspendedYield", record.arg === ContinueSentinel) continue; return { value: record.arg, done: context.done }; } "throw" === record.type && (state = "completed", context.method = "throw", context.arg = record.arg); } }; } function maybeInvokeDelegate(delegate, context) { var methodName = context.method, method = delegate.iterator[methodName]; if (undefined === method) return context.delegate = null, "throw" === methodName && delegate.iterator["return"] && (context.method = "return", context.arg = undefined, maybeInvokeDelegate(delegate, context), "throw" === context.method) || "return" !== methodName && (context.method = "throw", context.arg = new TypeError("The iterator does not provide a '" + methodName + "' method")), ContinueSentinel; var record = tryCatch(method, delegate.iterator, context.arg); if ("throw" === record.type) return context.method = "throw", context.arg = record.arg, context.delegate = null, ContinueSentinel; var info = record.arg; return info ? info.done ? (context[delegate.resultName] = info.value, context.next = delegate.nextLoc, "return" !== context.method && (context.method = "next", context.arg = undefined), context.delegate = null, ContinueSentinel) : info : (context.method = "throw", context.arg = new TypeError("iterator result is not an object"), context.delegate = null, ContinueSentinel); } function pushTryEntry(locs) { var entry = { tryLoc: locs[0] }; 1 in locs && (entry.catchLoc = locs[1]), 2 in locs && (entry.finallyLoc = locs[2], entry.afterLoc = locs[3]), this.tryEntries.push(entry); } function resetTryEntry(entry) { var record = entry.completion || {}; record.type = "normal", delete record.arg, entry.completion = record; } function Context(tryLocsList) { this.tryEntries = [{ tryLoc: "root" }], tryLocsList.forEach(pushTryEntry, this), this.reset(!0); } function values(iterable) { if (iterable) { var iteratorMethod = iterable[iteratorSymbol]; if (iteratorMethod) return iteratorMethod.call(iterable); if ("function" == typeof iterable.next) return iterable; if (!isNaN(iterable.length)) { var i = -1, next = function next() { for (; ++i < iterable.length;) { if (hasOwn.call(iterable, i)) return next.value = iterable[i], next.done = !1, next; } return next.value = undefined, next.done = !0, next; }; return next.next = next; } } return { next: doneResult }; } function doneResult() { return { value: undefined, done: !0 }; } return GeneratorFunction.prototype = GeneratorFunctionPrototype, defineProperty(Gp, "constructor", { value: GeneratorFunctionPrototype, configurable: !0 }), defineProperty(GeneratorFunctionPrototype, "constructor", { value: GeneratorFunction, configurable: !0 }), GeneratorFunction.displayName = define(GeneratorFunctionPrototype, toStringTagSymbol, "GeneratorFunction"), exports.isGeneratorFunction = function (genFun) { var ctor = "function" == typeof genFun && genFun.constructor; return !!ctor && (ctor === GeneratorFunction || "GeneratorFunction" === (ctor.displayName || ctor.name)); }, exports.mark = function (genFun) { return Object.setPrototypeOf ? Object.setPrototypeOf(genFun, GeneratorFunctionPrototype) : (genFun.__proto__ = GeneratorFunctionPrototype, define(genFun, toStringTagSymbol, "GeneratorFunction")), genFun.prototype = Object.create(Gp), genFun; }, exports.awrap = function (arg) { return { __await: arg }; }, defineIteratorMethods(AsyncIterator.prototype), define(AsyncIterator.prototype, asyncIteratorSymbol, function () { return this; }), exports.AsyncIterator = AsyncIterator, exports.async = function (innerFn, outerFn, self, tryLocsList, PromiseImpl) { void 0 === PromiseImpl && (PromiseImpl = Promise); var iter = new AsyncIterator(wrap(innerFn, outerFn, self, tryLocsList), PromiseImpl); return exports.isGeneratorFunction(outerFn) ? iter : iter.next().then(function (result) { return result.done ? result.value : iter.next(); }); }, defineIteratorMethods(Gp), define(Gp, toStringTagSymbol, "Generator"), define(Gp, iteratorSymbol, function () { return this; }), define(Gp, "toString", function () { return "[object Generator]"; }), exports.keys = function (val) { var object = Object(val), keys = []; for (var key in object) { keys.push(key); } return keys.reverse(), function next() { for (; keys.length;) { var key = keys.pop(); if (key in object) return next.value = key, next.done = !1, next; } return next.done = !0, next; }; }, exports.values = values, Context.prototype = { constructor: Context, reset: function reset(skipTempReset) { if (this.prev = 0, this.next = 0, this.sent = this._sent = undefined, this.done = !1, this.delegate = null, this.method = "next", this.arg = undefined, this.tryEntries.forEach(resetTryEntry), !skipTempReset) for (var name in this) { "t" === name.charAt(0) && hasOwn.call(this, name) && !isNaN(+name.slice(1)) && (this[name] = undefined); } }, stop: function stop() { this.done = !0; var rootRecord = this.tryEntries[0].completion; if ("throw" === rootRecord.type) throw rootRecord.arg; return this.rval; }, dispatchException: function dispatchException(exception) { if (this.done) throw exception; var context = this; function handle(loc, caught) { return record.type = "throw", record.arg = exception, context.next = loc, caught && (context.method = "next", context.arg = undefined), !!caught; } for (var i = this.tryEntries.length - 1; i >= 0; --i) { var entry = this.tryEntries[i], record = entry.completion; if ("root" === entry.tryLoc) return handle("end"); if (entry.tryLoc <= this.prev) { var hasCatch = hasOwn.call(entry, "catchLoc"), hasFinally = hasOwn.call(entry, "finallyLoc"); if (hasCatch && hasFinally) { if (this.prev < entry.catchLoc) return handle(entry.catchLoc, !0); if (this.prev < entry.finallyLoc) return handle(entry.finallyLoc); } else if (hasCatch) { if (this.prev < entry.catchLoc) return handle(entry.catchLoc, !0); } else { if (!hasFinally) throw new Error("try statement without catch or finally"); if (this.prev < entry.finallyLoc) return handle(entry.finallyLoc); } } } }, abrupt: function abrupt(type, arg) { for (var i = this.tryEntries.length - 1; i >= 0; --i) { var entry = this.tryEntries[i]; if (entry.tryLoc <= this.prev && hasOwn.call(entry, "finallyLoc") && this.prev < entry.finallyLoc) { var finallyEntry = entry; break; } } finallyEntry && ("break" === type || "continue" === type) && finallyEntry.tryLoc <= arg && arg <= finallyEntry.finallyLoc && (finallyEntry = null); var record = finallyEntry ? finallyEntry.completion : {}; return record.type = type, record.arg = arg, finallyEntry ? (this.method = "next", this.next = finallyEntry.finallyLoc, ContinueSentinel) : this.complete(record); }, complete: function complete(record, afterLoc) { if ("throw" === record.type) throw record.arg; return "break" === record.type || "continue" === record.type ? this.next = record.arg : "return" === record.type ? (this.rval = this.arg = record.arg, this.method = "return", this.next = "end") : "normal" === record.type && afterLoc && (this.next = afterLoc), ContinueSentinel; }, finish: function finish(finallyLoc) { for (var i = this.tryEntries.length - 1; i >= 0; --i) { var entry = this.tryEntries[i]; if (entry.finallyLoc === finallyLoc) return this.complete(entry.completion, entry.afterLoc), resetTryEntry(entry), ContinueSentinel; } }, "catch": function _catch(tryLoc) { for (var i = this.tryEntries.length - 1; i >= 0; --i) { var entry = this.tryEntries[i]; if (entry.tryLoc === tryLoc) { var record = entry.completion; if ("throw" === record.type) { var thrown = record.arg; resetTryEntry(entry); } return thrown; } } throw new Error("illegal catch attempt"); }, delegateYield: function delegateYield(iterable, resultName, nextLoc) { return this.delegate = { iterator: values(iterable), resultName: resultName, nextLoc: nextLoc }, "next" === this.method && (this.arg = undefined), ContinueSentinel; } }, exports; }
function asyncGeneratorStep(gen, resolve, reject, _next, _throw, key, arg) { try { var info = gen[key](arg); var value = info.value; } catch (error) { reject(error); return; } if (info.done) { resolve(value); } else { Promise.resolve(value).then(_next, _throw); } }
function _asyncToGenerator(fn) { return function () { var self = this, args = arguments; return new Promise(function (resolve, reject) { var gen = fn.apply(self, args); function _next(value) { asyncGeneratorStep(gen, resolve, reject, _next, _throw, "next", value); } function _throw(err) { asyncGeneratorStep(gen, resolve, reject, _next, _throw, "throw", err); } _next(undefined); }); }; }
function _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError("this hasn't been initialised - super() hasn't been called"); } return self; }
function _defineProperty(obj, key, value) { key = _toPropertyKey(key); if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }
function _toPropertyKey(arg) { var key = _toPrimitive(arg, "string"); return typeof key === "symbol" ? key : String(key); }
function _toPrimitive(input, hint) { if (typeof input !== "object" || input === null) return input; var prim = input[Symbol.toPrimitive]; if (prim !== undefined) { var res = prim.call(input, hint || "default"); if (typeof res !== "object") return res; throw new TypeError("@@toPrimitive must return a primitive value."); } return (hint === "string" ? String : Number)(input); }
function _inheritsLoose(subClass, superClass) { subClass.prototype = Object.create(superClass.prototype); subClass.prototype.constructor = subClass; _setPrototypeOf(subClass, superClass); }
function _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf ? Object.setPrototypeOf.bind() : function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }
function _extends() { _extends = Object.assign ? Object.assign.bind() : function (target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i]; for (var key in source) { if (Object.prototype.hasOwnProperty.call(source, key)) { target[key] = source[key]; } } } return target; }; return _extends.apply(this, arguments); }
var _default = (0, _withEditorProps.connectToEditor)(function (_ref) {
  var readOnly = _ref.readOnly,
    _ref$toolBar = _ref.toolBar,
    toolBar = _ref$toolBar === void 0 ? {} : _ref$toolBar;
  return {
    readOnly: readOnly,
    isOpen: toolBar.openItem === "alignmentTool"
  };
})(function (_ref2) {
  var toolbarItemProps = _ref2.toolbarItemProps,
    isOpen = _ref2.isOpen;
  return /*#__PURE__*/_react["default"].createElement(_ToolbarItem["default"], _extends({
    Icon: /*#__PURE__*/_react["default"].createElement(_core.Icon, {
      "data-test": "alignmentTool",
      icon: "align-left"
    }),
    // toggled: alignmentTool.isOpen,
    renderIconAbove: isOpen,
    // onIconClick: toggleFindTool,
    Dropdown: ConnectedAlignmentToolDropdown,
    onIconClick: "toggleDropdown",
    noDropdownIcon: true,
    tooltip: isOpen ? "Hide Alignment Tool" : "Align to This Sequence"
  }, toolbarItemProps));
});
exports["default"] = _default;
var AlignmentToolDropdown = /*#__PURE__*/function (_React$Component) {
  _inheritsLoose(AlignmentToolDropdown, _React$Component);
  function AlignmentToolDropdown() {
    return _React$Component.apply(this, arguments) || this;
  }
  var _proto = AlignmentToolDropdown.prototype;
  _proto.render = function render() {
    var _this = this;
    var _this$props = this.props,
      _this$props$savedAlig = _this$props.savedAlignments,
      savedAlignments = _this$props$savedAlig === void 0 ? [] : _this$props$savedAlig,
      hasSavedAlignments = _this$props.hasSavedAlignments,
      toggleDropdown = _this$props.toggleDropdown,
      sequenceData = _this$props.sequenceData;
    return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
      intent: _core.Intent.PRIMARY,
      onClick: function onClick() {
        toggleDropdown();
        (0, _GlobalDialogUtils.showDialog)({
          dialogType: "AlignmentToolDialog",
          props: {
            createNewAlignment: _this.props.createNewAlignment,
            upsertAlignmentRun: _this.props.upsertAlignmentRun,
            initialValues: {
              addedSequences: [_extends({}, sequenceData, {
                isTemplate: true
              })]
            }
          }
        });
      }
    }, "Create New Alignment"), /*#__PURE__*/_react["default"].createElement("br", null), /*#__PURE__*/_react["default"].createElement("br", null), /*#__PURE__*/_react["default"].createElement(_core.Callout, {
      intent: "warning"
    }, "Note: This tool requires an alignment server to be hooked up for it to work properly. It will NOT work in the OVE demo page."), /*#__PURE__*/_react["default"].createElement("div", {
      className: "vespacer"
    }), hasSavedAlignments && /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement("h6", null, "Saved Alignments:"), !savedAlignments.length && /*#__PURE__*/_react["default"].createElement("div", {
      style: {
        fontStyle: "italic"
      }
    }, " No Alignments"), savedAlignments.map(function (savedAlignment, i) {
      return /*#__PURE__*/_react["default"].createElement("div", {
        key: i
      }, "Saved Alignment ", i);
    })));
  };
  return AlignmentToolDropdown;
}(_react["default"].Component);
var ConnectedAlignmentToolDropdown = (0, _withEditorProps["default"])(AlignmentToolDropdown);
var AlignmentTool = /*#__PURE__*/function (_React$Component2) {
  _inheritsLoose(AlignmentTool, _React$Component2);
  function AlignmentTool() {
    var _this2;
    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
      args[_key] = arguments[_key];
    }
    _this2 = _React$Component2.call.apply(_React$Component2, [this].concat(args)) || this;
    _defineProperty(_assertThisInitialized(_this2), "state", {
      templateSeqIndex: 0
    });
    _defineProperty(_assertThisInitialized(_this2), "sendSelectedDataToBackendForAlignment", /*#__PURE__*/function () {
      var _ref3 = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(values) {
        var addedSequences, isPairwiseAlignment, isAlignToRefSeq, isAutotrimmedSeq, _this2$props, hideModal, createNewAlignment, upsertAlignmentRun, handleAlignment, templateSeqIndex, addedSequencesToUse, addedSequencesToUseTrimmed, i, _mottTrim, suggestedTrimStart, suggestedTrimEnd, elementsToTrim, element, seqsToAlign, alignmentId, replaceProtocol, alignmentDataToSend, _ref4, _alignedSequences, pairwiseAlignments, alignmentsToRefSeq, alignedSequences;
        return _regeneratorRuntime().wrap(function _callee$(_context) {
          while (1) {
            switch (_context.prev = _context.next) {
              case 0:
                addedSequences = values.addedSequences, isPairwiseAlignment = values.isPairwiseAlignment, isAlignToRefSeq = values.isAlignToRefSeq, isAutotrimmedSeq = values.isAutotrimmedSeq;
                _this2$props = _this2.props, hideModal = _this2$props.hideModal, createNewAlignment = _this2$props.createNewAlignment, upsertAlignmentRun = _this2$props.upsertAlignmentRun, handleAlignment = _this2$props.handleAlignment;
                templateSeqIndex = _this2.state.templateSeqIndex;
                addedSequencesToUse = (0, _array_move.array_move)(addedSequences, templateSeqIndex, 0);
                if (isAutotrimmedSeq) {
                  addedSequencesToUseTrimmed = (0, _lodash.cloneDeep)(addedSequencesToUse);
                  // trimming any sequences with chromatogram data
                  for (i = 0; i < addedSequencesToUseTrimmed.length; i++) {
                    if ("chromatogramData" in addedSequencesToUseTrimmed[i]) {
                      // if (addedSequencesToUseTrimmed[i].chromatogramData.qualNums) {
                      if ("qualNums" in addedSequencesToUseTrimmed[i].chromatogramData) {
                        // returning bp pos for { suggestedTrimStart, suggestedTrimEnd }
                        _mottTrim = mottTrim(addedSequencesToUseTrimmed[i].chromatogramData.qualNums), suggestedTrimStart = _mottTrim.suggestedTrimStart, suggestedTrimEnd = _mottTrim.suggestedTrimEnd;
                        addedSequencesToUseTrimmed[i].sequence = addedSequencesToUseTrimmed[i].sequence.slice(suggestedTrimStart, suggestedTrimEnd + 1);
                        elementsToTrim = ["baseCalls", "basePos", "qualNums"]; // eslint-disable-next-line no-unused-vars
                        for (element in addedSequencesToUseTrimmed[i].chromatogramData) {
                          if (elementsToTrim.indexOf(element) !== -1) {
                            addedSequencesToUseTrimmed[i].chromatogramData[element] = addedSequencesToUseTrimmed[i].chromatogramData[element].slice(suggestedTrimStart, suggestedTrimEnd + 1);
                          }
                        }
                      }
                    }
                  }
                }
                if (addedSequencesToUseTrimmed) {
                  seqsToAlign = addedSequencesToUseTrimmed;
                } else {
                  seqsToAlign = addedSequencesToUse;
                }
                hideModal();
                alignmentId = (0, _shortid["default"])(); // const alignmentIdMismatches = uniqid();
                createNewAlignment({
                  id: alignmentId,
                  name: seqsToAlign[0].name + " Alignment"
                });
                //set the alignment to loading
                upsertAlignmentRun({
                  id: alignmentId,
                  loading: true
                });
                // createNewMismatchesList({
                //   id: alignmentIdMismatches,
                //   name: addedSequencesToUse[0].name + " Mismatches",
                //   alignmentId: alignmentId
                // });

                // const j5server = process.env.REMOTE_J5 || "http://j5server.teselagen.com"

                window.toastr.success("Alignment submitted.");
                replaceProtocol = function replaceProtocol(url) {
                  return url.replace("http://", window.location.protocol + "//");
                };
                alignmentDataToSend = {
                  //only send over the bear necessities :)
                  sequencesToAlign: seqsToAlign,
                  isPairwiseAlignment: isPairwiseAlignment,
                  isAlignToRefSeq: isAlignToRefSeq
                };
                _context.next = 15;
                return handleAlignment;
              case 15:
                if (!_context.sent) {
                  _context.next = 19;
                  break;
                }
                _context.t0 = handleAlignment(alignmentDataToSend);
                _context.next = 24;
                break;
              case 19:
                _context.next = 21;
                return fetch({
                  url: replaceProtocol("http://j5server.teselagen.com/alignment/run"),
                  method: "post",
                  body: JSON.stringify(alignmentDataToSend)
                });
              case 21:
                _context.next = 23;
                return _context.sent.json();
              case 23:
                _context.t0 = _context.sent;
              case 24:
                _ref4 = _context.t0;
                _alignedSequences = _ref4.alignedSequences;
                pairwiseAlignments = _ref4.pairwiseAlignments;
                alignmentsToRefSeq = _ref4.alignmentsToRefSeq;
                // alignmentsToRefSeq set to alignedSequences for now
                alignedSequences = _alignedSequences;
                if (alignmentsToRefSeq) {
                  alignedSequences = alignmentsToRefSeq;
                }
                if (!alignedSequences && !pairwiseAlignments) window.toastr.error("Error running sequence alignment!");
                //set the alignment to loading
                upsertAlignmentRun({
                  id: alignmentId,
                  pairwiseAlignments: pairwiseAlignments && pairwiseAlignments.map(function (alignedSequences, topIndex) {
                    return alignedSequences.map(function (alignmentData, innerIndex) {
                      return {
                        sequenceData: seqsToAlign[innerIndex > 0 ? topIndex + 1 : 0],
                        alignmentData: alignmentData,
                        chromatogramData: seqsToAlign[innerIndex].chromatogramData
                      };
                    });
                  }),
                  alignmentTracks: alignedSequences && alignedSequences.map(function (alignmentData) {
                    return {
                      sequenceData: seqsToAlign[alignmentData.name.slice(0, alignmentData.name.indexOf("_"))],
                      alignmentData: alignmentData,
                      chromatogramData: seqsToAlign[alignmentData.name.slice(0, alignmentData.name.indexOf("_"))].chromatogramData
                    };
                  })
                  // alignmentTracks:
                  //   alignedSequences &&
                  //   alignedSequences.map((alignmentData, i) => {
                  //     return {
                  //       sequenceData: addedSequencesToUse[i],
                  //       alignmentData,
                  //       chromatogramData: addedSequencesToUse[i].chromatogramData
                  //     };
                  //   })
                });
              case 32:
              case "end":
                return _context.stop();
            }
          }
        }, _callee);
      }));
      return function (_x) {
        return _ref3.apply(this, arguments);
      };
    }());
    _defineProperty(_assertThisInitialized(_this2), "handleFileUpload", function (files, onChange) {
      var array = _this2.props.array;
      (0, _lodash.flatMap)(files, /*#__PURE__*/function () {
        var _ref5 = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee2(file) {
          var results;
          return _regeneratorRuntime().wrap(function _callee2$(_context2) {
            while (1) {
              switch (_context2.prev = _context2.next) {
                case 0:
                  _context2.next = 2;
                  return (0, _bioParsers.anyToJson)(file.originalFileObj, {
                    fileName: file.name,
                    acceptParts: true
                  });
                case 2:
                  results = _context2.sent;
                  return _context2.abrupt("return", results.forEach(function (result) {
                    if (result.success) {
                      array.push("addedSequences", result.parsedSequence);
                    } else {
                      return window.toastr.warning("Error parsing file: ", file.name);
                    }
                  }));
                case 4:
                case "end":
                  return _context2.stop();
              }
            }
          }, _callee2);
        }));
        return function (_x2) {
          return _ref5.apply(this, arguments);
        };
      }());
      onChange([]);
    });
    _defineProperty(_assertThisInitialized(_this2), "renderAddSequence", function (_ref6) {
      var fields = _ref6.fields,
        templateSeqIndex = _ref6.templateSeqIndex;
      var handleSubmit = _this2.props.handleSubmit;
      var sequencesToAlign = fields.getAll() || [];
      return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement("h6", null, "Or enter sequences in plain text format"), /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(AddYourOwnSeqForm, {
        addSeq: function addSeq(newSeq) {
          fields.push(newSeq);
        }
      }), /*#__PURE__*/_react["default"].createElement("h6", {
        style: {
          marginTop: 15
        }
      }, "Sequences To Align: "), !fields.getAll() && /*#__PURE__*/_react["default"].createElement("div", null, "No sequences added yet."), /*#__PURE__*/_react["default"].createElement("div", {
        style: {
          maxHeight: 180,
          overflowY: "auto"
        },
        className: "veAlignmentToolSelectedSequenceList"
      }, sequencesToAlign.map(function (addedSeq, index) {
        return /*#__PURE__*/_react["default"].createElement("div", {
          onClick: function onClick() {
            _this2.setState({
              templateSeqIndex: index
            });
          },
          style: {
            borderBottom: "1px solid lightgrey",
            paddingBottom: 4,
            marginBottom: 4,
            width: "100%",
            justifyContent: "space-between",
            alignItems: "center",
            display: "flex"
          },
          key: index
        }, /*#__PURE__*/_react["default"].createElement("div", null, addedSeq.name, " ", /*#__PURE__*/_react["default"].createElement("span", {
          style: {
            fontSize: 10
          }
        }, " ", "(", addedSeq.sequence.length, " bps)")), index === templateSeqIndex && /*#__PURE__*/_react["default"].createElement("div", {
          className: (0, _classnames["default"])(_core.Classes.TAG, _core.Classes.ROUND, _core.Classes.INTENT_PRIMARY)
        }, "template"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
          onClick: function onClick(e) {
            e.stopPropagation();
            e.preventDefault();
            fields.remove(index);
            if (index === templateSeqIndex) {
              _this2.setState({
                templateSeqIndex: 0
              });
            }
          }
        }, "Remove"));
      })), /*#__PURE__*/_react["default"].createElement("br", null), /*#__PURE__*/_react["default"].createElement(_teselagenReactComponents.CheckboxField, {
        name: "isPairwiseAlignment",
        style: {
          display: "flex",
          alignItems: "center"
        },
        label: /*#__PURE__*/_react["default"].createElement("div", null, "Create Pairwise Alignment", " ", /*#__PURE__*/_react["default"].createElement("span", {
          style: {
            fontSize: 11
          }
        }, "Individually align each uploaded file against the template sequence (instead of creating a single Multiple Sequence Alignment)"))
      }), /*#__PURE__*/_react["default"].createElement(_teselagenReactComponents.CheckboxField, {
        name: "isAlignToRefSeq",
        style: {
          display: "flex",
          alignItems: "center"
        },
        label: /*#__PURE__*/_react["default"].createElement("div", null, "Align Sequencing Reads to Reference Sequence", " ", /*#__PURE__*/_react["default"].createElement("span", {
          style: {
            fontSize: 11
          }
        }, "Align short sequencing reads to a long reference sequence"))
      }), /*#__PURE__*/_react["default"].createElement(_teselagenReactComponents.CheckboxField, {
        name: "isAutotrimmedSeq",
        style: {
          display: "flex",
          alignItems: "center"
        },
        label: /*#__PURE__*/_react["default"].createElement("div", null, "Auto-Trim Sequences", " ", /*#__PURE__*/_react["default"].createElement("span", {
          style: {
            fontSize: 11
          }
        }, "Automatically trim low-quality ends of sequences based on quality scores"))
      }), /*#__PURE__*/_react["default"].createElement(_core.Button, {
        style: {
          marginTop: 15,
          "float": "right"
        },
        intent: _core.Intent.PRIMARY,
        disabled: sequencesToAlign.length < 2,
        onClick: handleSubmit(_this2.sendSelectedDataToBackendForAlignment)
      }, "Create alignment")));
    });
    return _this2;
  }
  var _proto2 = AlignmentTool.prototype;
  _proto2.render = function render() {
    var selectFromSequenceLibraryHook = this.props.selectFromSequenceLibraryHook;
    var templateSeqIndex = this.state.templateSeqIndex;
    return /*#__PURE__*/_react["default"].createElement("div", {
      style: {
        padding: 20
      },
      className: "veAlignmentTool"
    }, /*#__PURE__*/_react["default"].createElement("h6", null, "Upload files you'd like to align (.ab1, .fasta, .gb) "), /*#__PURE__*/_react["default"].createElement(_teselagenReactComponents.FileUploadField, {
      name: "alignmentToolSequenceUpload",
      style: {
        maxWidth: 400
      },
      beforeUpload: this.handleFileUpload
    }), selectFromSequenceLibraryHook && /*#__PURE__*/_react["default"].createElement("h6", null, "Or Select from your sequence library "), /*#__PURE__*/_react["default"].createElement(_reduxForm.FieldArray, {
      name: "addedSequences",
      templateSeqIndex: templateSeqIndex,
      component: this.renderAddSequence
    }));
  };
  return AlignmentTool;
}(_react["default"].Component);
var AlignmentToolDialog = (0, _recompose.compose)((0, _teselagenReactComponents.wrapDialog)({
  title: "Create New Alignment"
}), (0, _reduxForm.reduxForm)({
  form: "veAlignmentTool"
}))(AlignmentTool);
exports.AlignmentToolDialog = AlignmentToolDialog;
var AddYourOwnSeqForm = (0, _reduxForm.reduxForm)({
  form: "AddYourOwnSeqForm",
  validate: function validate(_ref7) {
    var name = _ref7.name,
      sequence = _ref7.sequence;
    var errors = {};
    if (!name) {
      errors.name = "Required";
    }
    if (!sequence) {
      errors.sequence = "Required";
    }
    return errors;
  }
})(function (_ref8) {
  var pristine = _ref8.pristine,
    error = _ref8.error,
    handleSubmit = _ref8.handleSubmit,
    reset = _ref8.reset,
    addSeq = _ref8.addSeq;
  return /*#__PURE__*/_react["default"].createElement("form", {
    onSubmit: handleSubmit(function (vals) {
      reset();
      addSeq(vals);
    })
  }, /*#__PURE__*/_react["default"].createElement(_teselagenReactComponents.EditableTextField, {
    style: {
      maxWidth: 200
    },
    placeholder: "Untitled Sequence",
    name: "name"
  }), /*#__PURE__*/_react["default"].createElement(_teselagenReactComponents.TextareaField, {
    style: {
      maxWidth: 400
    },
    placeholder: "AGTTGAGC",
    name: "sequence"
  }), /*#__PURE__*/_react["default"].createElement(_core.Button, {
    disabled: pristine || error,
    type: "submit"
  }, "Add"));
});
function mottTrim(qualNums) {
  if (!qualNums) return;
  var startPos = 0;
  var endPos = 0;
  var totalScoreInfo = [];
  var score = 0;
  var totalScore = 0;
  var cutoff = 0.05;
  for (var i = 0; i < qualNums.length; i++) {
    // low-quality bases have high error probabilities, so may have a negative base score
    score = cutoff - Math.pow(10, qualNums[i] / -10);
    totalScore += score;
    totalScoreInfo.push(totalScore);
    // score = score + cutoff - Math.pow(10, qualNums[i] / -10);
    // if (totalScore < 0) {
    //   tempStart = i;
    // }
    // if (i - tempStart > endPos - startPos) {
    //   startPos = tempStart;
    //   endPos = i;
    // }
    if (totalScore < 0) {
      totalScore = 0;
    }
  }
  var firstPositiveValue = totalScoreInfo.find(function (e) {
    return e > 0;
  });
  startPos = totalScoreInfo.indexOf(firstPositiveValue);
  var highestValue = Math.max.apply(Math, totalScoreInfo);
  endPos = totalScoreInfo.lastIndexOf(highestValue);
  return {
    suggestedTrimStart: startPos,
    suggestedTrimEnd: endPos
  };
}