@jbrowse/plugin-linear-genome-view 2.1.0 → 2.1.3

package/dist/LinearGenomeView/components/OverviewRubberBand.js

@@ -22,43 +22,22 @@ 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 material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
-var util_1 = require("@jbrowse/core/util");
-var mobx_react_1 = require("mobx-react");
-var prop_types_1 = __importDefault(require("prop-types"));
-var __1 = require("..");
-var useStyles = (0, mui_1.makeStyles)()(function (theme) {
-    // @ts-ignore
-    var _a = theme.palette, tertiary = _a.tertiary, primary = _a.primary;
-    var background = tertiary
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const __1 = require("..");
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    const { tertiary, primary } = theme.palette;
+    const background = tertiary
         ? (0, material_1.alpha)(tertiary.main, 0.7)
         : (0, material_1.alpha)(primary.main, 0.7);
     return {
         rubberBand: {
             height: '100%',
-            background: background,
+            background,
             position: 'absolute',
             zIndex: 10,
             textAlign: 'center',
@@ -89,40 +68,35 @@ var useStyles = (0, mui_1.makeStyles)()(function (theme) {
         },
     };
 });
-var HoverTooltip = (0, mobx_react_1.observer)(function (_a) {
-    var _b;
-    var model = _a.model, open = _a.open, guideX = _a.guideX, overview = _a.overview;
-    var classes = useStyles().classes;
-    var cytobandOffset = model.cytobandOffset;
-    var assemblyManager = (0, util_1.getSession)(model).assemblyManager;
-    var px = overview.pxToBp(guideX - cytobandOffset);
-    var assembly = assemblyManager.get(px.assemblyName);
-    var cytoband = (_b = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _b === void 0 ? void 0 : _b.find(function (f) {
-        return px.coord > f.get('start') &&
-            px.coord < f.get('end') &&
-            px.refName === assembly.getCanonicalRefName(f.get('refName'));
-    });
+const HoverTooltip = (0, mobx_react_1.observer)(({ model, open, guideX, overview, }) => {
+    var _a;
+    const { classes } = useStyles();
+    const { cytobandOffset } = model;
+    const { assemblyManager } = (0, util_1.getSession)(model);
+    const px = overview.pxToBp(guideX - cytobandOffset);
+    const assembly = assemblyManager.get(px.assemblyName);
+    const cytoband = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.find(f => px.coord > f.get('start') &&
+        px.coord < f.get('end') &&
+        px.refName === assembly.getCanonicalRefName(f.get('refName')));
     return (react_1.default.createElement(material_1.Tooltip, { open: open, placement: "top", title: [(0, util_1.stringify)(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true },
         react_1.default.createElement("div", { className: classes.guide, style: {
                 left: guideX,
             } })));
 });
-function OverviewRubberBand(_a) {
-    var _b;
-    var model = _a.model, overview = _a.overview, _c = _a.ControlComponent, ControlComponent = _c === void 0 ? react_1.default.createElement("div", null) : _c;
-    var cytobandOffset = model.cytobandOffset;
-    var _d = __read((0, react_1.useState)(), 2), startX = _d[0], setStartX = _d[1];
-    var _e = __read((0, react_1.useState)(), 2), currentX = _e[0], setCurrentX = _e[1];
-    var _f = __read((0, react_1.useState)(), 2), guideX = _f[0], setGuideX = _f[1];
-    var controlsRef = (0, react_1.useRef)(null);
-    var rubberBandRef = (0, react_1.useRef)(null);
-    var classes = useStyles().classes;
-    var mouseDragging = startX !== undefined;
-    (0, react_1.useEffect)(function () {
+function OverviewRubberBand({ model, overview, ControlComponent = react_1.default.createElement("div", null), }) {
+    const { cytobandOffset } = model;
+    const [startX, setStartX] = (0, react_1.useState)();
+    const [currentX, setCurrentX] = (0, react_1.useState)();
+    const [guideX, setGuideX] = (0, react_1.useState)();
+    const controlsRef = (0, react_1.useRef)(null);
+    const rubberBandRef = (0, react_1.useRef)(null);
+    const { classes } = useStyles();
+    const mouseDragging = startX !== undefined;
+    (0, react_1.useEffect)(() => {
         function globalMouseMove(event) {
-            var ref = controlsRef.current;
+            const ref = controlsRef.current;
             if (ref && mouseDragging) {
-                var relativeX = event.clientX - ref.getBoundingClientRect().left;
+                const relativeX = event.clientX - ref.getBoundingClientRect().left;
                 setCurrentX(relativeX);
             }
         }
@@ -130,12 +104,14 @@ function OverviewRubberBand(_a) {
             // click and drag
             if (startX !== undefined && currentX !== undefined) {
                 if (Math.abs(currentX - startX) > 3) {
-                    model.moveTo(overview.pxToBp(startX - cytobandOffset), overview.pxToBp(currentX - cytobandOffset));
+                    const left = Math.min(startX, currentX);
+                    const right = Math.max(startX, currentX);
+                    model.moveTo(overview.pxToBp(left - cytobandOffset), overview.pxToBp(right - cytobandOffset));
                 }
             }
             // just a click
             if (startX !== undefined && currentX === undefined) {
-                var click = overview.pxToBp(startX - cytobandOffset);
+                const click = overview.pxToBp(startX - cytobandOffset);
                 if (!click.refName) {
                     (0, util_1.getSession)(model).notify('unknown position clicked');
                     console.error('unknown position clicked', click);
@@ -160,13 +136,13 @@ function OverviewRubberBand(_a) {
             window.addEventListener('mousemove', globalMouseMove, true);
             window.addEventListener('mouseup', globalMouseUp, true);
             window.addEventListener('keydown', globalKeyDown, true);
-            return function () {
+            return () => {
                 window.removeEventListener('mousemove', globalMouseMove, true);
                 window.removeEventListener('mouseup', globalMouseUp, true);
                 window.removeEventListener('keydown', globalKeyDown, true);
             };
         }
-        return function () { };
+        return () => { };
     }, [mouseDragging, currentX, startX, model, overview, cytobandOffset]);
     function mouseDown(event) {
         event.preventDefault();
@@ -188,21 +164,21 @@ function OverviewRubberBand(_a) {
             guideX !== undefined ? (react_1.default.createElement(HoverTooltip, { model: model, open: !mouseDragging, overview: overview, guideX: guideX })) : null,
             react_1.default.createElement("div", { className: classes.rubberBandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
     }
-    var left = startX || 0;
-    var width = 0;
+    let left = startX || 0;
+    let width = 0;
     if (startX !== undefined && currentX !== undefined) {
         left = currentX < startX ? currentX : startX;
         width = currentX - startX;
     }
     // calculate the start and end bp of drag
-    var leftBpOffset;
-    var rightBpOffset;
+    let leftBpOffset;
+    let rightBpOffset;
     if (startX) {
         leftBpOffset = overview.pxToBp(startX - cytobandOffset);
         rightBpOffset = overview.pxToBp(startX + width - cytobandOffset);
         if (currentX && currentX < startX) {
             ;
-            _b = __read([rightBpOffset, leftBpOffset], 2), leftBpOffset = _b[0], rightBpOffset = _b[1];
+            [leftBpOffset, rightBpOffset] = [rightBpOffset, leftBpOffset];
         }
     }
     return (react_1.default.createElement("div", { style: { position: 'relative' } },
@@ -228,19 +204,11 @@ function OverviewRubberBand(_a) {
                 }, keepMounted: true, disableRestoreFocus: true },
                 react_1.default.createElement(material_1.Typography, null, rightBpOffset ? (0, util_1.stringify)(rightBpOffset) : '')))) : null,
         react_1.default.createElement("div", { ref: rubberBandRef, className: classes.rubberBand, style: {
-                left: left,
+                left,
                 width: Math.abs(width),
                 height: __1.HEADER_OVERVIEW_HEIGHT,
             } }),
         react_1.default.createElement("div", { "data-testid": "rubberBand_controls", className: classes.rubberBandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
 }
-OverviewRubberBand.propTypes = {
-    model: mobx_react_1.PropTypes.objectOrObservableObject.isRequired,
-    overview: mobx_react_1.PropTypes.objectOrObservableObject.isRequired,
-    ControlComponent: prop_types_1.default.node,
-};
-OverviewRubberBand.defaultProps = {
-    ControlComponent: react_1.default.createElement("div", null),
-};
 exports.default = (0, mobx_react_1.observer)(OverviewRubberBand);
 //# sourceMappingURL=OverviewRubberBand.js.map

package/dist/LinearGenomeView/components/OverviewRubberBand.js.map

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+{"version":3,"file":"OverviewRubberBand.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/OverviewRubberBand.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAA0D;AAC1D,4CAAmE;AACnE,uCAA0C;AAC1C,6CAA0D;AAC1D,2CAAqC;AAErC,0BAAkE;AAIlE,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE;IACrC,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;IAC3C,MAAM,UAAU,GAAG,QAAQ;QACzB,CAAC,CAAC,IAAA,gBAAK,EAAC,QAAQ,CAAC,IAAI,EAAE,GAAG,CAAC;QAC3B,CAAC,CAAC,IAAA,gBAAK,EAAC,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;IAC5B,OAAO;QACL,UAAU,EAAE;YACV,MAAM,EAAE,MAAM;YACd,UAAU;YACV,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,EAAE;YACV,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,QAAQ;SACnB;QACD,iBAAiB,EAAE;YACjB,MAAM,EAAE,WAAW;YACnB,KAAK,EAAE,MAAM;YACb,SAAS,EAAE,CAAC;SACb;QACD,cAAc,EAAE;YACd,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,CAAC,OAAO,CAAC,YAAY;SAC/D;QACD,OAAO,EAAE;YACP,WAAW,EAAE,MAAM;YACnB,MAAM,EAAE,WAAW;SACpB;QACD,KAAK,EAAE;YACL,WAAW,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;YAC7B,YAAY,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;SAC/B;QACD,KAAK,EAAE;YACL,aAAa,EAAE,MAAM;YACrB,MAAM,EAAE,MAAM;YACd,KAAK,EAAE,CAAC;YACR,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,EAAE;SACX;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,IAAA,qBAAQ,EAC3B,CAAC,EACC,KAAK,EACL,IAAI,EACJ,MAAM,EACN,QAAQ,GAMT,EAAE,EAAE;;IACH,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IAE7C,MAAM,EAAE,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,GAAG,cAAc,CAAC,CAAA;IACnD,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,YAAY,CAAC,CAAA;IACrD,MAAM,QAAQ,GAAG,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,IAAI,CACxC,CAAC,CAAC,EAAE,CACF,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;QACzB,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;QACvB,EAAE,CAAC,OAAO,KAAK,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAChE,CAAA;IAED,OAAO,CACL,8BAAC,kBAAO,IACN,IAAI,EAAE,IAAI,EACV,SAAS,EAAC,KAAK,EACf,KAAK,EAAE,CAAC,IAAA,gBAAS,EAAC,EAAE,CAAC,EAAE,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EACvD,KAAK;QAEL,uCACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,MAAM;aACb,GACD,CACM,CACX,CAAA;AACH,CAAC,CACF,CAAA;AAED,SAAS,kBAAkB,CAAC,EAC1B,KAAK,EACL,QAAQ,EACR,gBAAgB,GAAG,0CAAO,GAK3B;IACC,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,GAAU,CAAA;IAC9C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,GAAU,CAAA;IAClD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,GAAU,CAAA;IAC9C,MAAM,WAAW,GAAG,IAAA,cAAM,EAAiB,IAAI,CAAC,CAAA;IAChD,MAAM,aAAa,GAAG,IAAA,cAAM,EAAiB,IAAI,CAAC,CAAA;IAClD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,aAAa,GAAG,MAAM,KAAK,SAAS,CAAA;IAE1C,IAAA,iBAAS,EAAC,GAAG,EAAE;QACb,SAAS,eAAe,CAAC,KAAiB;YACxC,MAAM,GAAG,GAAG,WAAW,CAAC,OAAO,CAAA;YAC/B,IAAI,GAAG,IAAI,aAAa,EAAE;gBACxB,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,GAAG,GAAG,CAAC,qBAAqB,EAAE,CAAC,IAAI,CAAA;gBAClE,WAAW,CAAC,SAAS,CAAC,CAAA;aACvB;QACH,CAAC;QAED,SAAS,aAAa;YACpB,iBAAiB;YACjB,IAAI,MAAM,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;gBAClD,IAAI,IAAI,CAAC,GAAG,CAAC,QAAQ,GAAG,MAAM,CAAC,GAAG,CAAC,EAAE;oBACnC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;oBACvC,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;oBACxC,KAAK,CAAC,MAAM,CACV,QAAQ,CAAC,MAAM,CAAC,IAAI,GAAG,cAAc,CAAC,EACtC,QAAQ,CAAC,MAAM,CAAC,KAAK,GAAG,cAAc,CAAC,CACxC,CAAA;iBACF;aACF;YAED,eAAe;YACf,IAAI,MAAM,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;gBAClD,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,GAAG,cAAc,CAAC,CAAA;gBACtD,IAAI,CAAC,KAAK,CAAC,OAAO,EAAE;oBAClB,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAC,MAAM,CAAC,0BAA0B,CAAC,CAAA;oBACpD,OAAO,CAAC,KAAK,CAAC,0BAA0B,EAAE,KAAK,CAAC,CAAA;iBACjD;qBAAM;oBACL,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,CAAA;iBACpE;aACF;YACD,SAAS,CAAC,SAAS,CAAC,CAAA;YACpB,WAAW,CAAC,SAAS,CAAC,CAAA;YAEtB,IAAI,MAAM,KAAK,SAAS,EAAE;gBACxB,SAAS,CAAC,SAAS,CAAC,CAAA;aACrB;QACH,CAAC;QAED,SAAS,aAAa,CAAC,KAAoB;YACzC,IAAI,KAAK,CAAC,GAAG,KAAK,QAAQ,EAAE;gBAC1B,SAAS,CAAC,SAAS,CAAC,CAAA;gBACpB,WAAW,CAAC,SAAS,CAAC,CAAA;aACvB;QACH,CAAC;QAED,IAAI,aAAa,EAAE;YACjB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;YAC3D,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,OAAO,GAAG,EAAE;gBACV,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;gBAC9D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;gBAC1D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YAC5D,CAAC,CAAA;SACF;QACD,OAAO,GAAG,EAAE,GAAE,CAAC,CAAA;IACjB,CAAC,EAAE,CAAC,aAAa,EAAE,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,cAAc,CAAC,CAAC,CAAA;IAEtE,SAAS,SAAS,CAAC,KAAuC;QACxD,KAAK,CAAC,cAAc,EAAE,CAAA;QACtB,KAAK,CAAC,eAAe,EAAE,CAAA;QACvB,IAAI,WAAW,CAAC,OAAO,EAAE;YACvB,SAAS,CACP,KAAK,CAAC,OAAO,GAAG,WAAW,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAC,IAAI,CACjE,CAAA;SACF;IACH,CAAC;IAED,SAAS,SAAS,CAAC,KAAuC;QACxD,IAAI,WAAW,CAAC,OAAO,EAAE;YACvB,SAAS,CACP,KAAK,CAAC,OAAO,GAAG,WAAW,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAC,IAAI,CACj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package/dist/LinearGenomeView/components/OverviewScaleBar.d.ts

@@ -28,10 +28,13 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         readonly initialized: boolean;
         readonly name: string;
         readonly aliases: string[];
+        readonly displayName: string | undefined;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
+        readonly lowerCaseRefNames: string[] | undefined;
+        readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
     } & {
@@ -62,17 +65,17 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
             forwardMap: {
-                [k: string]: string;
+                [key: string]: string;
             };
             reverseMap: {
-                [k: string]: string;
+                [key: string]: string;
             };
         }>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [k: string]: string;
+            [key: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [k: string]: string;
+            [key: string]: string;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
@@ -90,10 +93,13 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         readonly initialized: boolean;
         readonly name: string;
         readonly aliases: string[];
+        readonly displayName: string | undefined;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
+        readonly lowerCaseRefNames: string[] | undefined;
+        readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
     } & {
@@ -124,17 +130,17 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
             forwardMap: {
-                [k: string]: string;
+                [key: string]: string;
             };
             reverseMap: {
-                [k: string]: string;
+                [key: string]: string;
             };
         }>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [k: string]: string;
+            [key: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [k: string]: string;
+            [key: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;

package/dist/LinearGenomeView/components/OverviewScaleBar.js

@@ -1,49 +1,22 @@
 "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 __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 });
 exports.Polygon = exports.Cytobands = void 0;
-var react_1 = __importDefault(require("react"));
-var material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
-var mobx_react_1 = require("mobx-react");
-var Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
-var util_1 = require("@jbrowse/core/util");
-var blockTypes_1 = require("@jbrowse/core/util/blockTypes");
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
+const util_1 = require("@jbrowse/core/util");
+const blockTypes_1 = require("@jbrowse/core/util/blockTypes");
 // locals
-var __1 = require("..");
-var util_2 = require("../util");
-var OverviewRubberBand_1 = __importDefault(require("./OverviewRubberBand"));
-var wholeSeqSpacer = 2;
-var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
+const __1 = require("..");
+const util_2 = require("../util");
+const OverviewRubberBand_1 = __importDefault(require("./OverviewRubberBand"));
+const wholeSeqSpacer = 2;
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     scaleBar: {
         height: __1.HEADER_OVERVIEW_HEIGHT,
     },
@@ -57,11 +30,11 @@ var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
         height: __1.HEADER_OVERVIEW_HEIGHT,
     },
     scaleBarContigForward: {
-        backgroundImage: "url(\"data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M-.1 0L6 4.5L-.1 9' fill='none' stroke='%23ddd'/%3E%3C/svg%3E\")",
+        backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M-.1 0L6 4.5L-.1 9' fill='none' stroke='%23ddd'/%3E%3C/svg%3E")`,
         backgroundRepeat: 'repeat',
     },
     scaleBarContigReverse: {
-        backgroundImage: "url(\"data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M6 0L0 4.5L6 9' fill='none' stroke='%23ddd'/%3E%3C/svg%3E\")",
+        backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M6 0L0 4.5L6 9' fill='none' stroke='%23ddd'/%3E%3C/svg%3E")`,
         backgroundRepeat: 'repeat',
     },
     scaleBarRefName: {
@@ -92,30 +65,34 @@ var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
         width: '100%',
         position: 'absolute',
     },
-}); });
-var Polygon = (0, mobx_react_1.observer)(function (_a) {
-    var model = _a.model, overview = _a.overview, _b = _a.useOffset, useOffset = _b === void 0 ? true : _b;
-    var theme = (0, material_1.useTheme)();
-    var multiplier = Number(useOffset);
-    var interRegionPaddingWidth = model.interRegionPaddingWidth, offsetPx = model.offsetPx, dynamicBlocks = model.dynamicBlocks, cytobandOffset = model.cytobandOffset;
-    var contentBlocks = dynamicBlocks.contentBlocks, totalWidthPxWithoutBorders = dynamicBlocks.totalWidthPxWithoutBorders;
-    // @ts-ignore
-    var _c = theme.palette, tertiary = _c.tertiary, primary = _c.primary;
-    var polygonColor = tertiary ? tertiary.light : primary.light;
+}));
+const Polygon = (0, mobx_react_1.observer)(({ model, overview, useOffset = true, }) => {
+    const theme = (0, material_1.useTheme)();
+    const multiplier = Number(useOffset);
+    const { interRegionPaddingWidth, offsetPx, dynamicBlocks, cytobandOffset } = model;
+    const { contentBlocks, totalWidthPxWithoutBorders } = dynamicBlocks;
+    const { tertiary, primary } = theme.palette;
+    const polygonColor = tertiary ? tertiary.light : primary.light;
     if (!contentBlocks.length) {
         return null;
     }
-    var first = contentBlocks[0];
-    var last = contentBlocks[contentBlocks.length - 1];
-    var topLeft = (overview.bpToPx(__assign(__assign({}, first), { coord: first.reversed ? first.end : first.start })) || 0) +
+    const first = contentBlocks[0];
+    const last = contentBlocks[contentBlocks.length - 1];
+    const topLeft = (overview.bpToPx({
+        ...first,
+        coord: first.reversed ? first.end : first.start,
+    }) || 0) +
         cytobandOffset * multiplier;
-    var topRight = (overview.bpToPx(__assign(__assign({}, last), { coord: last.reversed ? last.start : last.end })) || 0) +
+    const topRight = (overview.bpToPx({
+        ...last,
+        coord: last.reversed ? last.start : last.end,
+    }) || 0) +
         cytobandOffset * multiplier;
-    var startPx = Math.max(0, -offsetPx);
-    var endPx = startPx +
+    const startPx = Math.max(0, -offsetPx);
+    const endPx = startPx +
         totalWidthPxWithoutBorders +
         (contentBlocks.length * interRegionPaddingWidth) / 2;
-    var points = [
+    const points = [
         [startPx, __1.HEADER_BAR_HEIGHT],
         [endPx, __1.HEADER_BAR_HEIGHT],
         [topRight, 0],
@@ -146,7 +123,7 @@ function leftRoundedRect(x, y, width, height, radius) {
         + "a" + radius + "," + radius + " 0 0 1 " + radius + "," + (-radius)
         + "z";
 }
-var colorMap = {
+const colorMap = {
     gneg: 'rgb(227,227,227)',
     gpos25: 'rgb(142,142,142)',
     gpos50: 'rgb(85,85,85)',
@@ -158,38 +135,36 @@ var colorMap = {
 };
 function getCytobands(assembly, refName) {
     var _a;
-    return (((_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.map(function (f) { return ({
+    return (((_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.map(f => ({
         refName: assembly.getCanonicalRefName(f.get('refName')),
         start: f.get('start'),
         end: f.get('end'),
         type: f.get('type'),
-    }); }).filter(function (f) { return f.refName === refName; })) || []);
+    })).filter(f => f.refName === refName)) || []);
 }
-var Cytobands = (0, mobx_react_1.observer)(function (_a) {
-    var overview = _a.overview, block = _a.block, assembly = _a.assembly;
-    var offsetPx = block.offsetPx, reversed = block.reversed;
-    var cytobands = getCytobands(assembly, block.refName);
-    var coords = cytobands.map(function (f) {
-        var refName = f.refName, start = f.start, end = f.end, type = f.type;
+const Cytobands = (0, mobx_react_1.observer)(({ overview, block, assembly, }) => {
+    const { offsetPx, reversed } = block;
+    const cytobands = getCytobands(assembly, block.refName);
+    const coords = cytobands.map(f => {
+        const { refName, start, end, type } = f;
         return [
             overview.bpToPx({
-                refName: refName,
+                refName,
                 coord: start,
             }),
             overview.bpToPx({
-                refName: refName,
+                refName,
                 coord: end,
             }),
             type,
         ];
     });
-    var arr = cytobands || [];
-    var lcap = reversed ? arr.length - 1 : 0;
-    var rcap = reversed ? 0 : arr.length - 1;
-    var firstCent = true;
-    return (react_1.default.createElement("g", { transform: "translate(-".concat(offsetPx, ")") }, coords.map(function (_a, index) {
-        var _b = __read(_a, 3), start = _b[0], end = _b[1], type = _b[2];
-        var key = "".concat(start, "-").concat(end, "-").concat(type);
+    const arr = cytobands || [];
+    const lcap = reversed ? arr.length - 1 : 0;
+    const rcap = reversed ? 0 : arr.length - 1;
+    let firstCent = true;
+    return (react_1.default.createElement("g", { transform: `translate(-${offsetPx})` }, coords.map(([start, end, type], index) => {
+        const key = `${start}-${end}-${type}`;
         if (type === 'acen' && firstCent) {
             firstCent = false;
             return (react_1.default.createElement("polygon", { key: key, points: [
@@ -217,21 +192,20 @@ var Cytobands = (0, mobx_react_1.observer)(function (_a) {
     })));
 });
 exports.Cytobands = Cytobands;
-var OverviewBox = (0, mobx_react_1.observer)(function (_a) {
-    var scale = _a.scale, model = _a.model, block = _a.block, overview = _a.overview;
-    var _b = useStyles(), classes = _b.classes, cx = _b.cx;
-    var cytobandOffset = model.cytobandOffset, bpPerPx = model.bpPerPx, showCytobands = model.showCytobands;
-    var start = block.start, end = block.end, reversed = block.reversed, refName = block.refName, assemblyName = block.assemblyName;
-    var majorPitch = (0, util_2.chooseGridPitch)(scale, 120, 15).majorPitch;
-    var assemblyManager = (0, util_1.getSession)(model).assemblyManager;
-    var assembly = assemblyManager.get(assemblyName);
-    var refNameColor = assembly === null || assembly === void 0 ? void 0 : assembly.getRefNameColor(refName);
-    var tickLabels = [];
-    for (var i = 0; i < Math.floor((end - start) / majorPitch); i++) {
-        var offsetLabel = (i + 1) * majorPitch;
+const OverviewBox = (0, mobx_react_1.observer)(({ scale, model, block, overview, }) => {
+    const { classes, cx } = useStyles();
+    const { cytobandOffset, bpPerPx, showCytobands } = model;
+    const { start, end, reversed, refName, assemblyName } = block;
+    const { majorPitch } = (0, util_2.chooseGridPitch)(scale, 120, 15);
+    const { assemblyManager } = (0, util_1.getSession)(model);
+    const assembly = assemblyManager.get(assemblyName);
+    const refNameColor = assembly === null || assembly === void 0 ? void 0 : assembly.getRefNameColor(refName);
+    const tickLabels = [];
+    for (let i = 0; i < Math.floor((end - start) / majorPitch); i++) {
+        const offsetLabel = (i + 1) * majorPitch;
         tickLabels.push(reversed ? end - offsetLabel : start + offsetLabel);
     }
-    var canDisplayCytobands = showCytobands && getCytobands(assembly, block.refName).length;
+    const canDisplayCytobands = showCytobands && getCytobands(assembly, block.refName).length;
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.Typography, { style: {
                 left: block.offsetPx + 3,
@@ -247,34 +221,38 @@ var OverviewBox = (0, mobx_react_1.observer)(function (_a) {
                 borderColor: refNameColor,
             } },
             !canDisplayCytobands
-                ? tickLabels.map(function (tickLabel, labelIdx) { return (react_1.default.createElement(material_1.Typography, { key: "".concat(JSON.stringify(block), "-").concat(tickLabel, "-").concat(labelIdx), className: classes.scaleBarLabel, variant: "body2", style: {
+                ? tickLabels.map((tickLabel, labelIdx) => (react_1.default.createElement(material_1.Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scaleBarLabel, variant: "body2", style: {
                         left: ((labelIdx + 1) * majorPitch) / scale,
                         pointerEvents: 'none',
                         color: refNameColor,
-                    } }, (0, util_1.getTickDisplayStr)(tickLabel, bpPerPx))); })
+                    } }, (0, util_1.getTickDisplayStr)(tickLabel, bpPerPx))))
                 : null,
             canDisplayCytobands ? (react_1.default.createElement("svg", { style: { width: '100%' } },
                 react_1.default.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }))) : null)));
 });
-var ScaleBar = (0, mobx_react_1.observer)(function (_a) {
-    var model = _a.model, scale = _a.scale, overview = _a.overview;
-    var classes = useStyles().classes;
-    var theme = (0, material_1.useTheme)();
-    var dynamicBlocks = model.dynamicBlocks, showCytobands = model.showCytobands, cytobandOffset = model.cytobandOffset;
-    var visibleRegions = dynamicBlocks.contentBlocks;
-    var overviewVisibleRegions = overview.dynamicBlocks;
-    // @ts-ignore
-    var _b = theme.palette, tertiary = _b.tertiary, primary = _b.primary;
-    var scaleBarColor = tertiary ? tertiary.light : primary.light;
+const ScaleBar = (0, mobx_react_1.observer)(({ model, scale, overview, }) => {
+    const { classes } = useStyles();
+    const theme = (0, material_1.useTheme)();
+    const { dynamicBlocks, showCytobands, cytobandOffset } = model;
+    const visibleRegions = dynamicBlocks.contentBlocks;
+    const overviewVisibleRegions = overview.dynamicBlocks;
+    const { tertiary, primary } = theme.palette;
+    const scaleBarColor = tertiary ? tertiary.light : primary.light;
     if (!visibleRegions.length) {
         return null;
     }
-    var first = visibleRegions[0];
-    var firstOverviewPx = overview.bpToPx(__assign(__assign({}, first), { coord: first.reversed ? first.end : first.start })) || 0;
-    var last = visibleRegions[visibleRegions.length - 1];
-    var lastOverviewPx = overview.bpToPx(__assign(__assign({}, last), { coord: last.reversed ? last.start : last.end })) || 0;
-    var color = showCytobands ? '#f00' : scaleBarColor;
-    var transparency = showCytobands ? 0.1 : 0.3;
+    const first = visibleRegions[0];
+    const firstOverviewPx = overview.bpToPx({
+        ...first,
+        coord: first.reversed ? first.end : first.start,
+    }) || 0;
+    const last = visibleRegions[visibleRegions.length - 1];
+    const lastOverviewPx = overview.bpToPx({
+        ...last,
+        coord: last.reversed ? last.start : last.end,
+    }) || 0;
+    const color = showCytobands ? '#f00' : scaleBarColor;
+    const transparency = showCytobands ? 0.1 : 0.3;
     return (react_1.default.createElement("div", { className: classes.scaleBar },
         react_1.default.createElement("div", { className: classes.scaleBarVisibleRegion, style: {
                 width: lastOverviewPx - firstOverviewPx,
@@ -282,28 +260,27 @@ var ScaleBar = (0, mobx_react_1.observer)(function (_a) {
                 background: (0, material_1.alpha)(color, transparency),
                 borderColor: color,
             } }),
-        overviewVisibleRegions.map(function (block, idx) {
-            return !(block instanceof blockTypes_1.ContentBlock) ? (react_1.default.createElement("div", { key: "".concat(JSON.stringify(block), "-").concat(idx), className: classes.scaleBarContig, style: {
+        overviewVisibleRegions.map((block, idx) => {
+            return !(block instanceof blockTypes_1.ContentBlock) ? (react_1.default.createElement("div", { key: `${JSON.stringify(block)}-${idx}`, className: classes.scaleBarContig, style: {
                     width: block.widthPx,
                     left: block.offsetPx,
                     backgroundColor: '#999',
                     backgroundImage: 'repeating-linear-gradient(90deg, transparent, transparent 1px, rgba(255,255,255,.5) 1px, rgba(255,255,255,.5) 3px)',
-                } })) : (react_1.default.createElement(OverviewBox, { scale: scale, block: block, model: model, overview: overview, key: "".concat(JSON.stringify(block), "-").concat(idx) }));
+                } })) : (react_1.default.createElement(OverviewBox, { scale: scale, block: block, model: model, overview: overview, key: `${JSON.stringify(block)}-${idx}` }));
         })));
 });
-function OverviewScaleBar(_a) {
-    var model = _a.model, children = _a.children;
-    var classes = useStyles().classes;
-    var totalBp = model.totalBp, width = model.width, cytobandOffset = model.cytobandOffset, displayedRegions = model.displayedRegions;
-    var overview = Base1DViewModel_1.default.create({
+function OverviewScaleBar({ model, children, }) {
+    const { classes } = useStyles();
+    const { totalBp, width, cytobandOffset, displayedRegions } = model;
+    const overview = Base1DViewModel_1.default.create({
         displayedRegions: JSON.parse(JSON.stringify(displayedRegions)),
         interRegionPaddingWidth: 0,
         minimumBlockWidth: model.minimumBlockWidth,
     });
-    var modWidth = width - cytobandOffset;
+    const modWidth = width - cytobandOffset;
     overview.setVolatileWidth(modWidth);
     overview.showAllRegions();
-    var scale = totalBp / (modWidth - (displayedRegions.length - 1) * wholeSeqSpacer);
+    const scale = totalBp / (modWidth - (displayedRegions.length - 1) * wholeSeqSpacer);
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(OverviewRubberBand_1.default, { model: model, overview: overview, ControlComponent: react_1.default.createElement(ScaleBar, { model: model, overview: overview, scale: scale }) }),
         react_1.default.createElement("div", { className: classes.overview },