@jbrowse/core 1.5.9 → 1.6.3

package/util/calculateStaticBlocks.test.js

@@ -1,12 +1,12 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
 var _calculateStaticBlocks = _interopRequireDefault(require("./calculateStaticBlocks"));
 
 describe('block calculation', function () {
   it('can calculate some blocks 1', function () {
-    var blocks1 = (0, _calculateStaticBlocks["default"])({
+    var blocks1 = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 0,
@@ -19,7 +19,7 @@ describe('block calculation', function () {
       minimumBlockWidth: 20,
       interRegionPaddingWidth: 2
     });
-    var blocks2 = (0, _calculateStaticBlocks["default"])({
+    var blocks2 = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 0,
@@ -36,7 +36,7 @@ describe('block calculation', function () {
     expect(blocks1).toEqual(blocks2);
   });
   it('can calculate some blocks 2', function () {
-    var blocks = (0, _calculateStaticBlocks["default"])({
+    var blocks = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 30,
@@ -57,7 +57,7 @@ describe('block calculation', function () {
     expect(blocks).toMatchSnapshot();
   });
   it('can calculate some blocks (should be empty because offscreen to the right)', function () {
-    var blockSet = (0, _calculateStaticBlocks["default"])({
+    var blockSet = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 2000,
@@ -78,7 +78,7 @@ describe('block calculation', function () {
     expect(blockSet.getBlocks()).toEqual([]);
   });
   it('can calculate some blocks (should be empty because offscreen to the left)', function () {
-    var blockSet = (0, _calculateStaticBlocks["default"])({
+    var blockSet = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: -2000,
@@ -99,7 +99,7 @@ describe('block calculation', function () {
     expect(blockSet.getBlocks()).toEqual([]);
   });
   it('can calculate some blocks 5', function () {
-    var blocks = (0, _calculateStaticBlocks["default"])({
+    var blocks = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 5000,
@@ -120,7 +120,7 @@ describe('block calculation', function () {
     expect(blocks).toMatchSnapshot();
   });
   it('can calculate some blocks 6', function () {
-    var blockSet = (0, _calculateStaticBlocks["default"])({
+    var blockSet = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 0,
@@ -142,7 +142,7 @@ describe('block calculation', function () {
     expect(blockSet.blocks[1].offsetPx).toBe(0);
   });
   it('can calculate some blocks 7', function () {
-    var blocks = (0, _calculateStaticBlocks["default"])({
+    var blocks = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 801,
@@ -163,7 +163,7 @@ describe('block calculation', function () {
     expect(blocks).toMatchSnapshot();
   });
   it('can calculate some blocks 8', function () {
-    var blocks = (0, _calculateStaticBlocks["default"])({
+    var blocks = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 1600,
@@ -184,7 +184,7 @@ describe('block calculation', function () {
     expect(blocks).toMatchSnapshot();
   });
   it('can calculate some blocks 9', function () {
-    var blockSet = (0, _calculateStaticBlocks["default"])({
+    var blockSet = (0, _calculateStaticBlocks.default)({
       width: 800,
       offsetPx: 1069,
       bpPerPx: 2,
@@ -205,7 +205,7 @@ describe('block calculation', function () {
     expect(blockSet).toMatchSnapshot();
   });
   it('can calculate some blocks 10', function () {
-    var blockSet = (0, _calculateStaticBlocks["default"])({
+    var blockSet = (0, _calculateStaticBlocks.default)({
       width: 800,
       offsetPx: 0,
       bpPerPx: 0.05,
@@ -230,7 +230,7 @@ describe('block calculation', function () {
 });
 describe('reverse block calculation', function () {
   test('1', function () {
-    var blocks = (0, _calculateStaticBlocks["default"])({
+    var blocks = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 0,
@@ -249,7 +249,7 @@ describe('reverse block calculation', function () {
 });
 describe('reversed displayed regions', function () {
   test('without elided region', function () {
-    var blocks = (0, _calculateStaticBlocks["default"])({
+    var blocks = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 0,
@@ -272,7 +272,7 @@ describe('reversed displayed regions', function () {
     expect(blocks).toMatchSnapshot();
   });
   test('with elided region', function () {
-    var blocks = (0, _calculateStaticBlocks["default"])({
+    var blocks = (0, _calculateStaticBlocks.default)({
       bpPerPx: 1,
       width: 800,
       offsetPx: 0,

package/util/compositeMap.js

@@ -1,32 +1,36 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
-var _createForOfIteratorHelper2 = _interopRequireDefault(require("@babel/runtime/helpers/esm/createForOfIteratorHelper"));
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/esm/classCallCheck"));
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/esm/createClass"));
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
+
+function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
+
+function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
 
 // takes an array or Map or Set (anything iterable with values()) of Maps
 // and lets you query them as one Map
 var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
   function CompositeMap(submaps) {
-    (0, _classCallCheck2["default"])(this, CompositeMap);
+    (0, _classCallCheck2.default)(this, CompositeMap);
     this.submaps = submaps;
   }
 
-  (0, _createClass2["default"])(CompositeMap, [{
+  (0, _createClass2.default)(CompositeMap, [{
     key: "has",
     value: function has(id) {
-      var _iterator = (0, _createForOfIteratorHelper2["default"])(this.submaps.values()),
+      var _iterator = _createForOfIteratorHelper(this.submaps.values()),
           _step;
 
       try {
@@ -48,7 +52,7 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
   }, {
     key: "get",
     value: function get(id) {
-      var _iterator2 = (0, _createForOfIteratorHelper2["default"])(this.submaps.values()),
+      var _iterator2 = _createForOfIteratorHelper(this.submaps.values()),
           _step2;
 
       try {
@@ -69,14 +73,14 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
     }
   }, {
     key: "values",
-    value: /*#__PURE__*/_regenerator["default"].mark(function values() {
+    value: /*#__PURE__*/_regenerator.default.mark(function values() {
       var _iterator3, _step3, key;
 
-      return _regenerator["default"].wrap(function values$(_context) {
+      return _regenerator.default.wrap(function values$(_context) {
         while (1) {
           switch (_context.prev = _context.next) {
             case 0:
-              _iterator3 = (0, _createForOfIteratorHelper2["default"])(this.keys());
+              _iterator3 = _createForOfIteratorHelper(this.keys());
               _context.prev = 1;
 
               _iterator3.s();
@@ -121,20 +125,20 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
     })
   }, {
     key: "keys",
-    value: /*#__PURE__*/_regenerator["default"].mark(function keys() {
+    value: /*#__PURE__*/_regenerator.default.mark(function keys() {
       var keys, _iterator4, _step4, submap, _iterator6, _step6, key, _iterator5, _step5, _key;
 
-      return _regenerator["default"].wrap(function keys$(_context2) {
+      return _regenerator.default.wrap(function keys$(_context2) {
         while (1) {
           switch (_context2.prev = _context2.next) {
             case 0:
               keys = new Set();
-              _iterator4 = (0, _createForOfIteratorHelper2["default"])(this.submaps.values());
+              _iterator4 = _createForOfIteratorHelper(this.submaps.values());
 
               try {
                 for (_iterator4.s(); !(_step4 = _iterator4.n()).done;) {
                   submap = _step4.value;
-                  _iterator6 = (0, _createForOfIteratorHelper2["default"])(submap.keys());
+                  _iterator6 = _createForOfIteratorHelper(submap.keys());
 
                   try {
                     for (_iterator6.s(); !(_step6 = _iterator6.n()).done;) {
@@ -153,7 +157,7 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
                 _iterator4.f();
               }
 
-              _iterator5 = (0, _createForOfIteratorHelper2["default"])(keys);
+              _iterator5 = _createForOfIteratorHelper(keys);
               _context2.prev = 4;
 
               _iterator5.s();
@@ -199,14 +203,14 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
   }, {
     key: "find",
     value: function find(f) {
-      var _iterator7 = (0, _createForOfIteratorHelper2["default"])(this.submaps.values()),
+      var _iterator7 = _createForOfIteratorHelper(this.submaps.values()),
           _step7;
 
       try {
         for (_iterator7.s(); !(_step7 = _iterator7.n()).done;) {
           var submap = _step7.value;
 
-          var _iterator8 = (0, _createForOfIteratorHelper2["default"])(submap.values()),
+          var _iterator8 = _createForOfIteratorHelper(submap.values()),
               _step8;
 
           try {
@@ -234,14 +238,14 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
     }
   }, {
     key: _Symbol$iterator,
-    value: /*#__PURE__*/_regenerator["default"].mark(function value() {
+    value: /*#__PURE__*/_regenerator.default.mark(function value() {
       var _iterator9, _step9, key;
 
-      return _regenerator["default"].wrap(function value$(_context3) {
+      return _regenerator.default.wrap(function value$(_context3) {
         while (1) {
           switch (_context3.prev = _context3.next) {
             case 0:
-              _iterator9 = (0, _createForOfIteratorHelper2["default"])(this.keys());
+              _iterator9 = _createForOfIteratorHelper(this.keys());
               _context3.prev = 1;
 
               _iterator9.s();
@@ -286,14 +290,14 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
     })
   }, {
     key: "entries",
-    value: /*#__PURE__*/_regenerator["default"].mark(function entries() {
+    value: /*#__PURE__*/_regenerator.default.mark(function entries() {
       var _iterator10, _step10, k;
 
-      return _regenerator["default"].wrap(function entries$(_context4) {
+      return _regenerator.default.wrap(function entries$(_context4) {
         while (1) {
           switch (_context4.prev = _context4.next) {
             case 0:
-              _iterator10 = (0, _createForOfIteratorHelper2["default"])(this.keys());
+              _iterator10 = _createForOfIteratorHelper(this.keys());
               _context4.prev = 1;
 
               _iterator10.s();
@@ -340,4 +344,4 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
   return CompositeMap;
 }(Symbol.iterator);
 
-exports["default"] = CompositeMap;
+exports.default = CompositeMap;

package/util/idMaker.js

@@ -1,13 +1,13 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault")["default"];
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = idMaker;
+exports.default = idMaker;
 
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/esm/typeof"));
+var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
 var _ = require("./");
 
@@ -26,7 +26,7 @@ function idMaker(args) {
       break;
     }
 
-    if ((0, _typeof2["default"])(args[key]) === 'object' && args[key]) {
+    if ((0, _typeof2.default)(args[key]) === 'object' && args[key]) {
       id += idMaker(args[key], id);
     } else {
       id += "".concat(key, "-").concat(args[key], ";");

package/util/index.d.ts

@@ -304,6 +304,28 @@ export declare const defaultCodonTable: {
 export declare function generateCodonTable(table: any): {
     [key: string]: string;
 };
-export declare function updateStatus(statusMsg: string, statusCallback: Function, fn: Function): Promise<any>;
+export declare function updateStatus<U>(msg: string, cb: (arg: string) => void, fn: () => U): Promise<U>;
 export declare function hashCode(str: string): number;
 export declare function objectHash(obj: Record<string, any>): string;
+export declare function bytesForRegions(regions: Region[], index: any): Promise<number>;
+export declare type ViewSnap = {
+    bpPerPx: number;
+    interRegionPaddingWidth: number;
+    minimumBlockWidth: number;
+    width: number;
+    displayedRegions: {
+        start: number;
+        end: number;
+        refName: string;
+        reversed: boolean;
+    }[];
+};
+export declare function viewBpToPx({ refName, coord, regionNumber, self, }: {
+    refName: string;
+    coord: number;
+    regionNumber?: number;
+    self: ViewSnap;
+}): {
+    index: number;
+    offsetPx: number;
+} | undefined;