@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,+DAAqD;AACrD,yCAA+C;AAC/C,uCAA0C;AAG1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,GAAG,EAAE,CAAC,CAAC;IACpC,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,UAAU,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,sDACe,WAAW,IAAA,uBAAO,EAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE9B,YAAY,CAAC,CAAC,CAAC,CACd;YACE,sDAAiB,sBAAsB;gBACrC,8BAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;YACN,8BAAC,iBAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;oBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;oBAC/D,OAAO,KAAK,CAAA;gBACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE;oBACL,GAAG;iBACJ,GACD,CACD,CACJ,CAAC,CAAC,CAAC,IAAI;QAEP,UAAU,CAAC,CAAC,CAAC,CACZ,sDACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,YAAY,CAAC,CAAC,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;aAClD;YAED,8BAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}

package/dist/LinearAlignmentsDisplay/index.js

@@ -3,17 +3,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 // locals
-var configSchema_1 = __importDefault(require("./models/configSchema"));
-var model_1 = __importDefault(require("./models/model"));
-var AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
+const configSchema_1 = __importDefault(require("./models/configSchema"));
+const model_1 = __importDefault(require("./models/model"));
+const AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
 function default_1(pluginManager) {
-    pluginManager.addDisplayType(function () {
-        var configSchema = (0, configSchema_1.default)(pluginManager);
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearAlignmentsDisplay',
-            configSchema: configSchema,
+            configSchema,
             stateModel: (0, model_1.default)(pluginManager, configSchema),
             trackType: 'AlignmentsTrack',
             viewType: 'LinearGenomeView',

package/dist/LinearAlignmentsDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearAlignmentsDisplay/index.ts"],"names":[],"mappings":";;;;;AAAA,kGAAyE;AAEzE,SAAS;AACT,yEAAuD;AACvD,2DAAyC;AACzC,uFAA2D;AAE3D,mBAAyB,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,yBAAyB;YAC/B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAd,2BAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,4BAYC"}

package/dist/LinearAlignmentsDisplay/models/configSchema.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-var configModelFactory = function (pluginManager) {
-    var PileupDisplayConfigSchema = pluginManager.getDisplayType('LinearPileupDisplay').configSchema;
-    var SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema;
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const configModelFactory = (pluginManager) => {
+    const PileupDisplayConfigSchema = pluginManager.getDisplayType('LinearPileupDisplay').configSchema;
+    const SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema;
     return (0, configuration_1.ConfigurationSchema)('LinearAlignmentsDisplay', {
         pileupDisplay: PileupDisplayConfigSchema,
         snpCoverageDisplay: SNPCoverageDisplayConfigSchema,

package/dist/LinearAlignmentsDisplay/models/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAAkF;AAGlF,MAAM,kBAAkB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC1D,MAAM,yBAAyB,GAAG,aAAa,CAAC,cAAc,CAC5D,qBAAqB,CACtB,CAAC,YAAY,CAAA;IACd,MAAM,8BAA8B,GAAG,aAAa,CAAC,cAAc,CACjE,0BAA0B,CAC3B,CAAC,YAAY,CAAA;IAEd,OAAO,IAAA,mCAAmB,EACxB,yBAAyB,EACzB;QACE,aAAa,EAAE,yBAAyB;QACxC,kBAAkB,EAAE,8BAA8B;KACnD,EACD,EAAE,iBAAiB,EAAE,yDAA6B,EAAE,eAAe,EAAE,IAAI,EAAE,CAC5E,CAAA;AACH,CAAC,CAAA;AAGD,kBAAe,kBAAkB,CAAA"}

package/dist/LinearAlignmentsDisplay/models/model.js

@@ -1,89 +1,17 @@
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importDefault(require("react"));
-var configuration_1 = require("@jbrowse/core/configuration");
-var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-var mobx_1 = require("mobx");
-var mobx_state_tree_1 = require("mobx-state-tree");
-var util_1 = require("@jbrowse/core/util");
-var fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-var minDisplayHeight = 20;
-var stateModelFactory = function (pluginManager, configSchema) {
+const react_1 = __importDefault(require("react"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_1 = require("@jbrowse/core/util");
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
+const minDisplayHeight = 20;
+const stateModelFactory = (pluginManager, configSchema) => {
     return mobx_state_tree_1.types
         .compose('LinearAlignmentsDisplay', models_1.BaseDisplay, mobx_state_tree_1.types.model({
         PileupDisplay: mobx_state_tree_1.types.maybe(pluginManager.getDisplayType('LinearPileupDisplay').stateModel),
@@ -96,35 +24,40 @@ var stateModelFactory = function (pluginManager, configSchema) {
         showPileup: true,
         userFeatureScreenDensity: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
     }))
-        .volatile(function () { return ({
+        .volatile(() => ({
         scrollTop: 0,
-    }); })
-        .actions(function (self) { return ({
-        toggleCoverage: function () {
+    }))
+        .actions(self => ({
+        toggleCoverage() {
             self.showCoverage = !self.showCoverage;
         },
-        togglePileup: function () {
+        togglePileup() {
             self.showPileup = !self.showPileup;
         },
-        setScrollTop: function (scrollTop) {
+        setScrollTop(scrollTop) {
             self.scrollTop = scrollTop;
         },
-        setSNPCoverageHeight: function (n) {
+        setSNPCoverageHeight(n) {
             self.snpCovHeight = n;
         },
-    }); })
-        .views(function (self) {
-        var superTrackMenuItems = self.trackMenuItems;
+    }))
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems } = self;
         return {
             get pileupDisplayConfig() {
-                var conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
-                var track = (0, util_1.getContainingTrack)(self);
-                return __assign(__assign({}, conf), { type: 'LinearPileupDisplay', name: "".concat((0, configuration_1.getConf)(track, 'name'), " pileup"), displayId: "".concat(self.configuration.displayId, "_pileup_xyz") });
+                const conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
+                const track = (0, util_1.getContainingTrack)(self);
+                return {
+                    ...conf,
+                    type: 'LinearPileupDisplay',
+                    name: `${(0, configuration_1.getConf)(track, 'name')} pileup`,
+                    displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
+                };
             },
-            getFeatureByID: function (blockKey, id) {
+            getFeatureByID(blockKey, id) {
                 return self.PileupDisplay.getFeatureByID(blockKey, id);
             },
-            searchFeatureByID: function (id) {
+            searchFeatureByID(id) {
                 return self.PileupDisplay.searchFeatureByID(id);
             },
             get features() {
@@ -144,12 +77,18 @@ var stateModelFactory = function (pluginManager, configSchema) {
                 return self.PileupDisplay.sortedByRefName;
             },
             get snpCoverageDisplayConfig() {
-                var conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
-                var track = (0, util_1.getContainingTrack)(self);
-                return __assign(__assign({}, conf), { type: 'LinearSNPCoverageDisplay', name: "".concat((0, configuration_1.getConf)(track, 'name'), " snp coverage"), displayId: "".concat(self.configuration.displayId, "_snpcoverage_xyz") });
+                const conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
+                const track = (0, util_1.getContainingTrack)(self);
+                return {
+                    ...conf,
+                    type: 'LinearSNPCoverageDisplay',
+                    name: `${(0, configuration_1.getConf)(track, 'name')} snp coverage`,
+                    displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
+                };
             },
-            trackMenuItems: function () {
-                return __spreadArray(__spreadArray([], __read(superTrackMenuItems()), false), [
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
                     {
                         type: 'subMenu',
                         label: 'Pileup settings',
@@ -160,29 +99,29 @@ var stateModelFactory = function (pluginManager, configSchema) {
                         label: 'SNPCoverage settings',
                         subMenu: self.SNPCoverageDisplay.trackMenuItems(),
                     },
-                ], false);
+                ];
             },
         };
     })
-        .actions(function (self) { return ({
-        setSNPCoverageDisplay: function (displayConfig) {
+        .actions(self => ({
+        setSNPCoverageDisplay(displayConfig) {
             self.SNPCoverageDisplay = {
                 type: 'LinearSNPCoverageDisplay',
                 configuration: displayConfig,
                 height: self.snpCovHeight,
             };
         },
-        setUserFeatureScreenDensity: function (limit) {
+        setUserFeatureScreenDensity(limit) {
             self.PileupDisplay.setUserFeatureScreenDensity(limit);
             self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit);
         },
-        setPileupDisplay: function (displayConfig) {
+        setPileupDisplay(displayConfig) {
             self.PileupDisplay = {
                 type: 'LinearPileupDisplay',
                 configuration: displayConfig,
             };
         },
-        setHeight: function (displayHeight) {
+        setHeight(displayHeight) {
             if (displayHeight > minDisplayHeight) {
                 self.height = displayHeight;
             }
@@ -191,15 +130,15 @@ var stateModelFactory = function (pluginManager, configSchema) {
             }
             return self.height;
         },
-        resizeHeight: function (distance) {
-            var oldHeight = self.height;
-            var newHeight = this.setHeight(self.height + distance);
+        resizeHeight(distance) {
+            const oldHeight = self.height;
+            const newHeight = this.setHeight(self.height + distance);
             return newHeight - oldHeight;
         },
-    }); })
-        .actions(function (self) { return ({
-        afterAttach: function () {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(function () {
+    }))
+        .actions(self => ({
+        afterAttach() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 if (!self.SNPCoverageDisplay) {
                     self.setSNPCoverageDisplay(self.snpCoverageDisplayConfig);
                 }
@@ -227,36 +166,21 @@ var stateModelFactory = function (pluginManager, configSchema) {
                     self.SNPCoverageDisplay.setColorBy((0, mobx_state_tree_1.getSnapshot)(self.PileupDisplay.colorBy));
                 }
             }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(function () {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 self.setSNPCoverageHeight(self.SNPCoverageDisplay.height);
             }));
         },
-        renderSvg: function (opts) {
-            return __awaiter(this, void 0, void 0, function () {
-                var pileupHeight, _a, _b, _c, _d, _e, _f, _g, _h, _j;
-                return __generator(this, function (_k) {
-                    switch (_k.label) {
-                        case 0:
-                            pileupHeight = self.height - self.SNPCoverageDisplay.height;
-                            return [4 /*yield*/, (0, mobx_1.when)(function () { return self.PileupDisplay.ready; })];
-                        case 1:
-                            _k.sent();
-                            _b = (_a = react_1.default).createElement;
-                            _c = [react_1.default.Fragment, null];
-                            _e = (_d = react_1.default).createElement;
-                            _f = ["g", null];
-                            return [4 /*yield*/, self.SNPCoverageDisplay.renderSvg(opts)];
-                        case 2:
-                            _c = _c.concat([_e.apply(_d, _f.concat([_k.sent()]))]);
-                            _h = (_g = react_1.default).createElement;
-                            _j = ["g", { transform: "translate(0 ".concat(self.SNPCoverageDisplay.height, ")") }];
-                            return [4 /*yield*/, self.PileupDisplay.renderSvg(__assign(__assign({}, opts), { overrideHeight: pileupHeight }))];
-                        case 3: return [2 /*return*/, (_b.apply(_a, _c.concat([_h.apply(_g, _j.concat([_k.sent()]))])))];
-                    }
-                });
-            });
+        async renderSvg(opts) {
+            const pileupHeight = self.height - self.SNPCoverageDisplay.height;
+            await (0, mobx_1.when)(() => self.PileupDisplay.ready);
+            return (react_1.default.createElement(react_1.default.Fragment, null,
+                react_1.default.createElement("g", null, await self.SNPCoverageDisplay.renderSvg(opts)),
+                react_1.default.createElement("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})` }, await self.PileupDisplay.renderSvg({
+                    ...opts,
+                    overrideHeight: pileupHeight,
+                }))));
         },
-    }); });
+    }));
 };
 exports.default = stateModelFactory;
 //# sourceMappingURL=model.js.map

package/dist/LinearAlignmentsDisplay/models/model.js.map

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package/dist/LinearPileupDisplay/components/ColorByModifications.js

@@ -1,39 +1,14 @@
 "use strict";
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importDefault(require("react"));
-var mobx_react_1 = require("mobx-react");
-var material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
-var Close_1 = __importDefault(require("@mui/icons-material/Close"));
-var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     closeButton: {
         position: 'absolute',
         right: theme.spacing(1),
@@ -47,27 +22,23 @@ var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
             padding: theme.spacing(1),
         },
     },
-}); });
-function ModificationTable(_a) {
-    var modifications = _a.modifications;
-    var classes = useStyles().classes;
+}));
+function ModificationTable({ modifications, }) {
+    const { classes } = useStyles();
     return (react_1.default.createElement("table", { className: classes.table },
-        react_1.default.createElement("tbody", null, modifications.map(function (_a) {
-            var _b = __read(_a, 2), key = _b[0], value = _b[1];
-            return (react_1.default.createElement("tr", { key: key },
-                react_1.default.createElement("td", null, key),
-                react_1.default.createElement("td", null, value),
-                react_1.default.createElement("td", { style: {
-                        width: '1em',
-                        background: value,
-                    } })));
-        }))));
+        react_1.default.createElement("tbody", null, modifications.map(([key, value]) => (react_1.default.createElement("tr", { key: key },
+            react_1.default.createElement("td", null, key),
+            react_1.default.createElement("td", null, value),
+            react_1.default.createElement("td", { style: {
+                    width: '1em',
+                    background: value,
+                } })))))));
 }
 function ColorByTagDlg(props) {
-    var classes = useStyles().classes;
-    var model = props.model, handleClose = props.handleClose;
-    var colorBy = model.colorBy, modificationTagMap = model.modificationTagMap;
-    var modifications = __spreadArray([], __read(modificationTagMap.entries()), false);
+    const { classes } = useStyles();
+    const { model, handleClose } = props;
+    const { colorBy, modificationTagMap } = model;
+    const modifications = [...modificationTagMap.entries()];
     return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
         react_1.default.createElement(material_1.DialogTitle, null,
             "Color by modifications",
@@ -79,7 +50,7 @@ function ColorByTagDlg(props) {
             react_1.default.createElement("div", { style: { margin: 20 } },
                 (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications' ? (react_1.default.createElement("div", null, modifications.length ? (react_1.default.createElement(react_1.default.Fragment, null,
                     "Current modification-type-to-color mapping",
-                    react_1.default.createElement(ModificationTable, { modifications: __spreadArray([], __read(modificationTagMap.entries()), false) }))) : (react_1.default.createElement("div", null,
+                    react_1.default.createElement(ModificationTable, { modifications: [...modificationTagMap.entries()] }))) : (react_1.default.createElement("div", null,
                     react_1.default.createElement(material_1.Typography, null, "Note: color by modifications is already enabled. Loading current modifications..."),
                     react_1.default.createElement(material_1.CircularProgress, { size: 15 }))))) : null,
                 (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? (react_1.default.createElement(ModificationTable, { modifications: [
@@ -87,19 +58,19 @@ function ColorByTagDlg(props) {
                         ['unmethylated', 'blue'],
                     ] })) : null),
             react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: function () {
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: () => {
                         model.setColorScheme({
                             type: 'modifications',
                         });
                         handleClose();
                     } }, "Modifications"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: function () {
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: () => {
                         model.setColorScheme({
                             type: 'methylation',
                         });
                         handleClose();
                     } }, "Methylation"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", style: { margin: 5 }, onClick: function () { return handleClose(); } }, "Cancel")))));
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", style: { margin: 5 }, onClick: () => handleClose() }, "Cancel")))));
 }
 exports.default = (0, mobx_react_1.observer)(ColorByTagDlg);
 //# sourceMappingURL=ColorByModifications.js.map

package/dist/LinearPileupDisplay/components/ColorByModifications.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ColorByModifications.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByModifications.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,4CASsB;AACtB,uCAA0C;AAC1C,sEAAiD;AAEjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;IACD,KAAK,EAAE;QACL,MAAM,EAAE,gBAAgB;QACxB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACxB,MAAM,EAAE;YACN,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;SAC1B;KACF;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EACzB,aAAa,GAGd;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,yCAAO,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,6CACG,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACnC,sCAAI,GAAG,EAAE,GAAG;YACV,0CAAK,GAAG,CAAM;YACd,0CAAK,KAAK,CAAM;YAChB,sCACE,KAAK,EAAE;oBACL,KAAK,EAAE,KAAK;oBACZ,UAAU,EAAE,KAAK;iBAClB,GACD,CACC,CACN,CAAC,CACI,CACF,CACT,CAAA;AACH,CAAC;AAED,SAAS,aAAa,CAAC,KAOtB;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAE7C,MAAM,aAAa,GAAG,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,CAAA;IAEvD,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,8BAAC,sBAAW;;YAEV,8BAAC,qBAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,8BAAC,eAAS,OAAG,CACF,CACD;QACd,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,oRAKE;YACb,8BAAC,qBAAU,yIAGE;YACb,uCAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;gBACvB,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,CAAC,CAAC,CAAC,CACnC,2CACG,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CACtB;;oBAEE,8BAAC,iBAAiB,IAChB,aAAa,EAAE,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,GAChD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,8BAAC,qBAAU,4FAGE;oBACb,8BAAC,2BAAgB,IAAC,IAAI,EAAE,EAAE,GAAI,CAC1B,CACP,CACG,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAC,CAAC,CAAC,CACjC,8BAAC,iBAAiB,IAChB,aAAa,EAAE;wBACb,CAAC,YAAY,EAAE,KAAK,CAAC;wBACrB,CAAC,cAAc,EAAE,MAAM,CAAC;qBACzB,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ;YACN,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,eAAe;yBACtB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,oBAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,aAAa;yBACpB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,kBAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,aAAa,CAAC,CAAA"}

package/dist/LinearPileupDisplay/components/ColorByTag.js

@@ -22,32 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importStar(require("react"));
-var mobx_react_1 = require("mobx-react");
-var material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
-var Close_1 = __importDefault(require("@mui/icons-material/Close"));
-var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
+const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     root: {
         width: 300,
     },
@@ -57,12 +41,12 @@ var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
         top: theme.spacing(1),
         color: theme.palette.grey[500],
     },
-}); });
+}));
 function ColorByTagDlg(props) {
-    var classes = useStyles().classes;
-    var model = props.model, handleClose = props.handleClose;
-    var _a = __read((0, react_1.useState)(''), 2), tag = _a[0], setTag = _a[1];
-    var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
+    const { classes } = useStyles();
+    const { model, handleClose } = props;
+    const [tag, setTag] = (0, react_1.useState)('');
+    const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
     return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
         react_1.default.createElement(material_1.DialogTitle, null,
             "Color by tag",
@@ -71,15 +55,15 @@ function ColorByTagDlg(props) {
         react_1.default.createElement(material_1.DialogContent, { style: { overflowX: 'hidden' } },
             react_1.default.createElement(material_1.Typography, null, "Enter tag to color by: "),
             react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),
-            react_1.default.createElement(material_1.TextField, { value: tag, onChange: function (event) { return setTag(event.target.value); }, placeholder: "Enter tag name", inputProps: {
+            react_1.default.createElement(material_1.TextField, { value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
                     maxLength: 2,
                     'data-testid': 'color-tag-name-input',
                 }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", "data-testid": "color-tag-name" }),
             react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: function () {
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
                         model.setColorScheme({
                             type: 'tag',
-                            tag: tag,
+                            tag,
                         });
                         handleClose();
                     }, disabled: !validTag }, "Submit"),

package/dist/LinearPileupDisplay/components/ColorByTag.js.map

@@ -1 +1 @@
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