@jbrowse/core 2.1.7 → 2.2.0

package/ui/AboutDialog.js

@@ -33,6 +33,7 @@ const material_1 = require("@mui/material");
 const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const mui_1 = require("tss-react/mui");
 const configuration_1 = require("../configuration");
+const LoadingEllipses_1 = __importDefault(require("./LoadingEllipses"));
 const util_1 = require("../util");
 const tracks_1 = require("../util/tracks");
 const BaseFeatureDetail_1 = require("../BaseFeatureWidget/BaseFeatureDetail");
@@ -86,7 +87,7 @@ function FileInfo({ config }) {
                 .replace(/>/g, '&gt;')}</pre>`,
         }
         : info || {};
-    return info !== null ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "File info" }, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : info === undefined ? ('Loading file data...') : (react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: details })))) : null;
+    return info !== null ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "File info" }, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : info === undefined ? (react_1.default.createElement(LoadingEllipses_1.default, { message: "Loading file data" })) : (react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: details })))) : null;
 }
 exports.FileInfo = FileInfo;
 function AboutContents({ config }) {

package/ui/App.js

@@ -38,6 +38,7 @@ const configuration_1 = require("../configuration");
 const DrawerWidget_1 = __importDefault(require("./DrawerWidget"));
 const DropDownMenu_1 = __importDefault(require("./DropDownMenu"));
 const ErrorMessage_1 = __importDefault(require("./ErrorMessage"));
+const LoadingEllipses_1 = __importDefault(require("./LoadingEllipses"));
 const EditableTypography_1 = __importDefault(require("./EditableTypography"));
 const Logo_1 = require("./Logo");
 const Snackbar_1 = __importDefault(require("./Snackbar"));
@@ -139,10 +140,12 @@ const ViewLauncher = (0, mobx_react_1.observer)(({ session }) => {
     const [value, setValue] = (0, react_1.useState)((_a = viewTypes[0]) === null || _a === void 0 ? void 0 : _a.name);
     return (react_1.default.createElement(material_1.Paper, { className: classes.selectPaper },
         react_1.default.createElement(material_1.Typography, null, "Select a view to launch"),
-        react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, viewTypes.map(({ name }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, name)))),
-        react_1.default.createElement(material_1.Button, { onClick: () => {
-                session.addView(value, {});
-            }, variant: "contained", color: "primary" }, "Launch view")));
+        react_1.default.createElement(material_1.FormControl, { style: { margin: 2 } },
+            react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, viewTypes.map(({ name }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, name))))),
+        react_1.default.createElement(material_1.FormControl, { style: { margin: 2 } },
+            react_1.default.createElement(material_1.Button, { onClick: () => {
+                    session.addView(value, {});
+                }, variant: "contained", color: "primary" }, "Launch view"))));
 });
 const ViewPanel = (0, mobx_react_1.observer)(({ view, session }) => {
     const { pluginManager } = (0, mobx_state_tree_1.getEnv)(session);
@@ -152,7 +155,7 @@ const ViewPanel = (0, mobx_react_1.observer)(({ view, session }) => {
     }
     const { ReactComponent } = viewType;
     return (react_1.default.createElement(ViewContainer_1.default, { view: view, onClose: () => session.removeView(view) },
-        react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null, "Loading...") },
+        react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(LoadingEllipses_1.default, null) },
             react_1.default.createElement(ReactComponent, { model: view, session: session, getTrackType: pluginManager.getTrackType }))));
 });
 const App = (0, mobx_react_1.observer)((props) => {

package/ui/AssemblySelector.js

@@ -55,7 +55,7 @@ const AssemblySelector = (0, mobx_react_1.observer)(({ session, onChange, select
         }
     }, [selection, onChange, selected]);
     const error = assemblyNames.length ? '' : 'No configured assemblies';
-    return (react_1.default.createElement(material_1.TextField, { select: true, label: "Assembly", variant: "outlined", helperText: error || 'Select assembly to view', value: error ? '' : selection, inputProps: { 'data-testid': 'assembly-selector' }, onChange: event => setLastSelected(event.target.value), error: !!error, InputProps: InputProps, disabled: !!error, className: classes.importFormEntry }, assemblyNames.map(name => {
+    return (react_1.default.createElement(material_1.TextField, { select: true, label: "Assembly", variant: "outlined", helperText: error || 'Select assembly to view', value: selection, inputProps: { 'data-testid': 'assembly-selector' }, onChange: event => setLastSelected(event.target.value), error: !!error, InputProps: InputProps, disabled: !!error, className: classes.importFormEntry }, assemblyNames.map(name => {
         const assembly = assemblyManager.get(name);
         const displayName = assembly ? (0, configuration_1.getConf)(assembly, 'displayName') : '';
         return (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName || name));

package/ui/DrawerWidget.js

@@ -32,6 +32,7 @@ const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const util_1 = require("../util");
+const LoadingEllipses_1 = __importDefault(require("./LoadingEllipses"));
 // icons
 const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
 const Close_1 = __importDefault(require("@mui/icons-material/Close"));
@@ -123,7 +124,7 @@ const DrawerWidget = (0, mobx_react_1.observer)(({ session }) => {
     const [toolbarHeight, setToolbarHeight] = (0, react_1.useState)(0);
     return (react_1.default.createElement(Drawer_1.default, { session: session },
         react_1.default.createElement(DrawerHeader, { session: session, setToolbarHeight: setToolbarHeight }),
-        react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null, "Loading...") },
+        react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(LoadingEllipses_1.default, null) },
             react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: ({ error }) => react_1.default.createElement(ErrorMessage_1.default, { error: error }) }, DrawerComponent ? (react_1.default.createElement(DrawerComponent, { model: visibleWidget, session: session, toolbarHeight: toolbarHeight })) : null))));
 });
 exports.default = DrawerWidget;

package/ui/LoadingEllipses.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { TypographyProps } from '@mui/material';
+interface Props extends TypographyProps {
+    message?: string;
+}
+export default function LoadingEllipses({ message, variant, ...rest }: Props): JSX.Element;
+export {};

package/ui/LoadingEllipses.js

@@ -0,0 +1,38 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const tss_react_1 = require("tss-react");
+const useStyles = (0, mui_1.makeStyles)()({
+    dots: {
+        '&::after': {
+            display: 'inline-block',
+            content: '""',
+            width: '1em',
+            textAlign: 'left',
+            animation: `${(0, tss_react_1.keyframes) `
+      0% {
+        content: '';
+      }
+      25% {
+          content: '.';
+      }
+      50% {
+        content: '..';
+      }
+      75% {
+        content: '...';
+      }
+      `} 1.4s infinite ease-in-out`,
+        },
+    },
+});
+function LoadingEllipses({ message = 'Loading', variant = 'body2', ...rest }) {
+    const { classes } = useStyles();
+    return (react_1.default.createElement(material_1.Typography, { className: classes.dots, ...rest, variant: variant }, `${message || 'Loading'}`));
+}
+exports.default = LoadingEllipses;

package/ui/index.d.ts

@@ -14,4 +14,5 @@ export { default as FatalErrorDialog } from './FatalErrorDialog';
 export { default as Menu } from './Menu';
 export { default as CascadingMenu } from './CascadingMenu';
 export { default as SanitizedHTML } from './SanitizedHTML';
+export { default as LoadingEllipses } from './LoadingEllipses';
 export * from './Menu';

package/ui/index.js

@@ -17,7 +17,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SanitizedHTML = exports.CascadingMenu = exports.Menu = exports.FatalErrorDialog = exports.Tooltip = exports.FactoryResetDialog = exports.EditableTypography = exports.ResizeHandle = exports.PrerenderedCanvas = exports.FileSelector = exports.AssemblySelector = exports.ErrorMessage = exports.ReturnToImportFormDialog = exports.App = exports.Logomark = exports.LogoFull = void 0;
+exports.LoadingEllipses = exports.SanitizedHTML = exports.CascadingMenu = exports.Menu = exports.FatalErrorDialog = exports.Tooltip = exports.FactoryResetDialog = exports.EditableTypography = exports.ResizeHandle = exports.PrerenderedCanvas = exports.FileSelector = exports.AssemblySelector = exports.ErrorMessage = exports.ReturnToImportFormDialog = exports.App = exports.Logomark = exports.LogoFull = void 0;
 __exportStar(require("./theme"), exports);
 var Logo_1 = require("./Logo");
 Object.defineProperty(exports, "LogoFull", { enumerable: true, get: function () { return Logo_1.LogoFull; } });
@@ -50,4 +50,6 @@ var CascadingMenu_1 = require("./CascadingMenu");
 Object.defineProperty(exports, "CascadingMenu", { enumerable: true, get: function () { return __importDefault(CascadingMenu_1).default; } });
 var SanitizedHTML_1 = require("./SanitizedHTML");
 Object.defineProperty(exports, "SanitizedHTML", { enumerable: true, get: function () { return __importDefault(SanitizedHTML_1).default; } });
+var LoadingEllipses_1 = require("./LoadingEllipses");
+Object.defineProperty(exports, "LoadingEllipses", { enumerable: true, get: function () { return __importDefault(LoadingEllipses_1).default; } });
 __exportStar(require("./Menu"), exports);

package/util/Base1DUtils.js

@@ -26,10 +26,16 @@ function moveTo(self, start, end) {
     if (!start || !end) {
         return;
     }
-    const { width, interRegionPaddingWidth } = self;
+    const { width, interRegionPaddingWidth, displayedRegions, bpPerPx, minimumBlockWidth, } = self;
     const len = lengthBetween(self, start, end);
-    const numBlocks = end.index - start.index;
-    const targetBpPerPx = len / (width - interRegionPaddingWidth * numBlocks);
+    let numBlocksWideEnough = 0;
+    for (let i = start.index; i < end.index; i++) {
+        const r = displayedRegions[i];
+        if ((r.end - r.start) / bpPerPx > minimumBlockWidth) {
+            numBlocksWideEnough++;
+        }
+    }
+    const targetBpPerPx = len / (width - interRegionPaddingWidth * numBlocksWideEnough);
     const newBpPerPx = self.zoomTo(targetBpPerPx);
     // If our target bpPerPx was smaller than the allowed minBpPerPx, adjust
     // the scroll so the requested range is in the middle of the screen

package/util/calculateDynamicBlocks.js

@@ -75,7 +75,7 @@ function calculateDynamicBlocks(model, padding = true, elision = true) {
                 isRightEndOfDisplayedRegion,
                 key: '',
             };
-            blockData.key = `${(0, _1.assembleLocString)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
+            blockData.key = `${(0, _1.assembleLocStringFast)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
             if (padding && blocks.length === 0 && isLeftEndOfDisplayedRegion) {
                 blocks.push(new blockTypes_1.InterRegionPaddingBlock({
                     key: `${blockData.key}-beforeFirstRegion`,

package/util/calculateStaticBlocks.js

@@ -59,7 +59,7 @@ function calculateStaticBlocks(model, padding = true, elision = true, extra = 0,
                 isRightEndOfDisplayedRegion,
                 key: '',
             };
-            blockData.key = `${(0, _1.assembleLocString)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
+            blockData.key = `${(0, _1.assembleLocStringFast)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
             if (padding && regionNumber === 0 && blockNum === 0) {
                 blocks.push(new blockTypes_1.InterRegionPaddingBlock({
                     key: `${blockData.key}-beforeFirstRegion`,

package/util/index.d.ts

@@ -63,6 +63,7 @@ export declare function getContainingDisplay(node: IAnyStateTreeNode): import(".
  * ```
  */
 export declare function assembleLocString(region: ParsedLocString): string;
+export declare function assembleLocStringFast(region: ParsedLocString, cb?: (n: number) => string | number): string;
 export interface ParsedLocString {
     assemblyName?: string;
     refName: string;

package/util/index.js

@@ -29,8 +29,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getBpDisplayStr = exports.supportedIndexingAdapters = exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useDebounce = exports.inProduction = exports.inDevelopment = exports.isFeature = exports.SimpleFeature = void 0;
-exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = void 0;
+exports.supportedIndexingAdapters = exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useDebounce = exports.inProduction = exports.inDevelopment = exports.isFeature = exports.SimpleFeature = void 0;
+exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -237,11 +237,18 @@ exports.getContainingDisplay = getContainingDisplay;
  * ```
  */
 function assembleLocString(region) {
+    return assembleLocStringFast(region, toLocale);
+}
+exports.assembleLocString = assembleLocString;
+// same as assembleLocString above, but does not perform toLocaleString which
+// can slow down the speed of block calculations which use assembleLocString
+// for block.key
+function assembleLocStringFast(region, cb = (n) => n) {
     const { assemblyName, refName, start, end, reversed } = region;
     const assemblyNameString = assemblyName ? `{${assemblyName}}` : '';
     let startString;
     if (start !== undefined) {
-        startString = `:${(start + 1).toLocaleString('en-US')}`;
+        startString = `:${cb(start + 1)}`;
     }
     else if (end !== undefined) {
         startString = ':1';
@@ -251,10 +258,7 @@ function assembleLocString(region) {
     }
     let endString;
     if (end !== undefined) {
-        endString =
-            start !== undefined && start + 1 === end
-                ? ''
-                : `..${end.toLocaleString('en-US')}`;
+        endString = start !== undefined && start + 1 === end ? '' : `..${cb(end)}`;
     }
     else {
         endString = start !== undefined ? '..' : '';
@@ -265,7 +269,7 @@ function assembleLocString(region) {
     }
     return `${assemblyNameString}${refName}${startString}${endString}${rev}`;
 }
-exports.assembleLocString = assembleLocString;
+exports.assembleLocStringFast = assembleLocStringFast;
 function parseLocStringOneBased(locString, isValidRefName) {
     if (!locString) {
         throw new Error('no location string provided, could not parse');
@@ -649,7 +653,7 @@ function minmax(a, b) {
 exports.minmax = minmax;
 function stringify({ refName, coord, oob, }) {
     return refName
-        ? `${refName}:${coord.toLocaleString('en-US')}${oob ? ' (out of bounds)' : ''}`
+        ? `${refName}:${toLocale(coord)}${oob ? ' (out of bounds)' : ''}`
         : '';
 }
 exports.stringify = stringify;

package/util/io/RemoteFileWithRangeCache.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="node" />
 import { RemoteFile, PolyfilledResponse } from 'generic-filehandle';
-interface BinaryRangeResponse {
+export interface BinaryRangeResponse {
     headers: Record<string, string>;
     requestDate: Date;
     responseDate: Date;
@@ -14,4 +14,3 @@ export declare class RemoteFileWithRangeCache extends RemoteFile {
         signal?: AbortSignal;
     }): Promise<BinaryRangeResponse>;
 }
-export {};

package/util/layouts/GranularRectLayout.d.ts

@@ -9,6 +9,11 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
     private maxHeight;
     private displayMode;
     private pTotalHeight;
+    /**
+     * pitchX - layout grid pitch in the X direction
+     * pitchY - layout grid pitch in the Y direction
+     * maxHeight - maximum layout height, default Infinity (no max)
+     */
     constructor({ pitchX, pitchY, maxHeight, hardRowLimit, displayMode, }?: {
         pitchX?: number;
         pitchY?: number;
@@ -33,9 +38,9 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
      */
     discardRange(left: number, right: number): void;
     hasSeen(id: string): boolean;
-    getByCoord(x: number, y: number): Record<string, T> | string | undefined;
+    getByCoord(x: number, y: number): string | Record<string, T> | undefined;
     getByID(id: string): RectTuple | undefined;
-    getDataByID(id: string): unknown;
+    getDataByID(id: string): T | undefined;
     cleanup(): void;
     getTotalHeight(): number;
     get totalHeight(): number;

package/util/layouts/GranularRectLayout.js

@@ -18,66 +18,47 @@ class LayoutRow {
     constructor() {
         this.padding = 1;
         this.widthLimit = 1000000;
-        // this.rowState.offset is the offset of the bits array relative to the genomic coordinates
-        //      (modified by pitchX, but we don't know that in this class)
-        // this.rowState.bits is the array of items in the layout row, indexed by (x - this.offset)
-        // this.rowState.min is the leftmost edge of all the rectangles we have in the layout
-        // this.rowState.max is the rightmost edge of all the rectangles we have in the layout
     }
-    // log(msg: string): void {
-    //   // if (this.rowNumber === 0)
-    //   // eslint-disable-next-line no-console
-    //   console.log(`r${this.rowNumber}: ${msg}`)
-    // }
+    // this.rowState.bits is the array of items in the layout row, indexed by (x - this.offset)
+    // this.rowState.min is the leftmost edge of all the rectangles we have in the layout
+    // this.rowState.max is the rightmost edge of all the rectangles we have in the layout
+    // this.rowState.offset is the offset of the bits array relative to the genomic coordinates
+    //      (modified by pitchX, but we don't know that in this class)
     setAllFilled(data) {
         this.allFilled = data;
     }
     getItemAt(x) {
+        var _a;
         if (this.allFilled) {
             return this.allFilled;
         }
-        if (!this.rowState) {
-            return undefined;
-        }
-        if (this.rowState.min === undefined) {
+        if (((_a = this.rowState) === null || _a === void 0 ? void 0 : _a.min) === undefined ||
+            x < this.rowState.min ||
+            x >= this.rowState.max) {
             return undefined;
         }
-        if (x < this.rowState.min) {
-            return undefined;
-        }
-        if (x >= this.rowState.max) {
-            return undefined;
-        }
-        const offset = x - this.rowState.offset;
-        // if (offset < 0)
-        //     debugger
-        // if (offset >= this.rowState.bits.length)
-        //     debugger
-        return this.rowState.bits[offset];
+        return this.rowState.bits[x - this.rowState.offset];
     }
     isRangeClear(left, right) {
         if (this.allFilled) {
             return false;
         }
-        if (!this.rowState) {
-            return true;
-        }
-        const { min, max } = this.rowState;
-        if (right <= min || left >= max) {
+        if (this.rowState === undefined ||
+            right <= this.rowState.min ||
+            left >= this.rowState.max) {
             return true;
         }
-        // TODO: check right and middle before looping
-        const maxX = Math.min(max, right);
-        let x = Math.max(min, left);
-        for (; x < right && x < maxX; x += 1) {
-            if (this.getItemAt(x)) {
-                return false;
-            }
+        const { min, max, offset, bits } = this.rowState;
+        const maxX = Math.min(max, right) - offset;
+        let flag = true;
+        for (let x = Math.max(min, left) - offset; x < maxX && flag; x++) {
+            flag = bits[x] === undefined;
         }
-        return true;
+        return flag;
     }
+    // NOTE: this.rowState.min, this.rowState.max, and this.rowState.offset are
+    // interbase coordinates
     initialize(left, right) {
-        // NOTE: this.rowState.min, this.rowState.max, and this.rowState.offset are interbase coordinates
         const rectWidth = right - left;
         return {
             offset: left - rectWidth,
@@ -85,7 +66,6 @@ class LayoutRow {
             max: right,
             bits: new Array(3 * rectWidth),
         };
-        // this.log(`initialize ${this.rowState.min} - ${this.rowState.max} (${this.rowState.bits.length})`)
     }
     addRect(rect, data) {
         const left = rect.l;
@@ -220,8 +200,7 @@ class LayoutRow {
     }
 }
 class GranularRectLayout {
-    /*
-     *
+    /**
      * pitchX - layout grid pitch in the X direction
      * pitchY - layout grid pitch in the Y direction
      * maxHeight - maximum layout height, default Infinity (no max)
@@ -296,7 +275,7 @@ class GranularRectLayout {
         const maxY = top + rect.h;
         for (let y = top; y < maxY; y += 1) {
             const row = bitmap[y];
-            if (row && !row.isRangeClear(rect.l, rect.r)) {
+            if (row !== undefined && !row.isRangeClear(rect.l, rect.r)) {
                 return true;
             }
         }
@@ -370,7 +349,12 @@ class GranularRectLayout {
         const r = this.rectangles.get(id);
         if (r) {
             const t = r.top * this.pitchY;
-            return [r.l * this.pitchX, t, r.r * this.pitchX, t + r.originalHeight];
+            return [
+                r.l * this.pitchX,
+                t,
+                r.r * this.pitchX,
+                t + r.originalHeight,
+            ];
         }
         return undefined;
     }

package/util/layouts/MultiLayout.d.ts

@@ -1,14 +1,14 @@
 import { BaseLayout, SerializedLayout } from './BaseLayout';
 export default class MultiLayout<SUB_LAYOUT_CLASS extends BaseLayout<T>, T> {
     SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS;
-    subLayouts: Map<string, SUB_LAYOUT_CLASS>;
     subLayoutConstructorArgs: Record<string, any>;
+    subLayouts: Map<string, SUB_LAYOUT_CLASS>;
     /**
      * layout class that just keeps a number of named sub-layouts.
      * basically just a fancier
      * `{ layout1: new GranularRectLayout(), layout2: new GranularRectLayout() ...}`
      */
-    constructor(SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS, layoutArgs?: Record<string, any>);
+    constructor(SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS, subLayoutConstructorArgs?: Record<string, any>);
     getDataByID(id: string): unknown;
     getSublayout(layoutName: string): SUB_LAYOUT_CLASS;
     addRect(layoutName: string, id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;

package/util/layouts/MultiLayout.js

@@ -6,12 +6,10 @@ class MultiLayout {
      * basically just a fancier
      * `{ layout1: new GranularRectLayout(), layout2: new GranularRectLayout() ...}`
      */
-    constructor(SubLayoutClass, layoutArgs = {}) {
+    constructor(SubLayoutClass, subLayoutConstructorArgs = {}) {
         this.SubLayoutClass = SubLayoutClass;
+        this.subLayoutConstructorArgs = subLayoutConstructorArgs;
         this.subLayouts = new Map();
-        this.subLayoutConstructorArgs = {};
-        this.subLayouts = new Map();
-        this.subLayoutConstructorArgs = layoutArgs;
     }
     getDataByID(id) {
         for (const layout of this.subLayouts.values()) {
@@ -36,8 +34,8 @@ class MultiLayout {
         return this.getSublayout(layoutName).addRect(id, left, right, height, data);
     }
     discardRange(layoutName, left, right) {
-        const layout = this.subLayouts.get(layoutName);
-        return layout && layout.discardRange(left, right);
+        var _a;
+        return (_a = this.subLayouts.get(layoutName)) === null || _a === void 0 ? void 0 : _a.discardRange(left, right);
     }
     toJSON() {
         const data = {};

package/util/simpleFeature.d.ts

@@ -31,6 +31,9 @@ export interface Feature {
      * Get an array of child features, or undefined if none.
      */
     children(): Feature[] | undefined;
+    /**
+     * Convert to JSON
+     */
     toJSON(): SimpleFeatureSerialized;
 }
 export declare function isFeature(thing: unknown): thing is Feature;

package/util/stats.d.ts

@@ -14,8 +14,34 @@ export interface FeatureStats extends UnrectifiedFeatureStats {
     scoreMean: number;
     scoreStdDev: number;
 }
+/**
+ * calculate standard deviation using the 'shortcut method' that accepts
+ * the sum and the sum squares of the elements
+ *
+ * @param sum - sum(i, 1..n)
+ * @param sumSquares - sum(i^2, 1..n)
+ * @param n - number of elements
+ * @param population - boolean: use population instead of sample correction
+ * @returns - the estimated std deviation
+ */
 export declare function calcStdFromSums(sum: number, sumSquares: number, n: number, population?: boolean): number;
+/**
+ * @param stats - a summary stats object with scoreSum, featureCount, scoreSumSquares, and basesCovered
+ * @returns - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
+ */
 export declare function rectifyStats(s: UnrectifiedFeatureStats): FeatureStats;
+/**
+ * calculates per-base scores for variable width features over a region
+ * @param region - object contains start, end
+ * @param features - list of features with start, end, score
+ * @returns array of numeric scores
+ */
 export declare function calcPerBaseStats(region: NoAssemblyRegion, features: Feature[]): number[];
+/**
+ * transform a list of scores to summary statistics
+ * @param region - object with start, end
+ * @param features - array of features which are possibly summary features
+ * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
+ */
 export declare function scoresToStats(region: NoAssemblyRegion, features: Observable<Feature>): Promise<FeatureStats>;
 export declare function blankStats(): FeatureStats;

package/util/stats.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.blankStats = exports.scoresToStats = exports.calcPerBaseStats = exports.rectifyStats = exports.calcStdFromSums = void 0;
 const operators_1 = require("rxjs/operators");
-/*
+/**
  * calculate standard deviation using the 'shortcut method' that accepts
  * the sum and the sum squares of the elements
  *
@@ -10,7 +10,7 @@ const operators_1 = require("rxjs/operators");
  * @param sumSquares - sum(i^2, 1..n)
  * @param n - number of elements
  * @param population - boolean: use population instead of sample correction
- * @return the estimated std deviation
+ * @returns - the estimated std deviation
  */
 function calcStdFromSums(sum, sumSquares, n, population = false) {
     if (n === 0) {
@@ -30,9 +30,9 @@ function calcStdFromSums(sum, sumSquares, n, population = false) {
     return variance < 0 ? 0 : Math.sqrt(variance);
 }
 exports.calcStdFromSums = calcStdFromSums;
-/*
+/**
  * @param stats - a summary stats object with scoreSum, featureCount, scoreSumSquares, and basesCovered
- * @return - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
+ * @returns - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
  */
 function rectifyStats(s) {
     return {
@@ -43,11 +43,11 @@ function rectifyStats(s) {
     };
 }
 exports.rectifyStats = rectifyStats;
-/*
+/**
  * calculates per-base scores for variable width features over a region
  * @param region - object contains start, end
  * @param features - list of features with start, end, score
- * @return array of numeric scores
+ * @returns array of numeric scores
  */
 function calcPerBaseStats(region, features) {
     const { start, end } = region;
@@ -76,11 +76,11 @@ function calcPerBaseStats(region, features) {
     return scores;
 }
 exports.calcPerBaseStats = calcPerBaseStats;
-/*
+/**
  * transform a list of scores to summary statistics
  * @param region - object with start, end
- * @param feats - array of features which are possibly summary features
- * @return - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
+ * @param features - array of features which are possibly summary features
+ * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
  */
 async function scoresToStats(region, features) {
     const { start, end } = region;