@jbrowse/plugin-linear-genome-view 2.10.2 → 2.11.0

package/dist/LinearGenomeView/components/Highlight.js

@@ -0,0 +1,126 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const colord_1 = require("@jbrowse/core/util/colord");
+const util_1 = require("@jbrowse/core/util");
+const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+// icons
+const Link_1 = __importDefault(require("@mui/icons-material/Link"));
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const Bookmark_1 = __importDefault(require("@mui/icons-material/Bookmark"));
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    var _a, _b;
+    return ({
+        highlight: {
+            height: '100%',
+            position: 'absolute',
+            overflow: 'hidden',
+            background: `${(0, colord_1.colord)((_b = (_a = theme.palette.highlight) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod')
+                .alpha(0.35)
+                .toRgbString()}`,
+        },
+    });
+});
+const Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlight, }) {
+    var _a, _b, _c;
+    const { classes } = useStyles();
+    const [open, setOpen] = (0, react_1.useState)(false);
+    const anchorEl = (0, react_1.useRef)(null);
+    const color = (_b = (_a = (0, material_1.useTheme)().palette.highlight) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod';
+    const session = (0, util_1.getSession)(model);
+    const { assemblyManager } = session;
+    const dismissHighlight = () => {
+        model.removeHighlight(highlight);
+    };
+    const menuItems = [
+        {
+            label: 'Dismiss highlight',
+            icon: Close_1.default,
+            onClick: () => dismissHighlight(),
+        },
+        {
+            label: 'Bookmark highlighted region',
+            icon: Bookmark_1.default,
+            onClick: () => {
+                let bookmarkWidget = session.widgets.get('GridBookmark');
+                if (!bookmarkWidget) {
+                    bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
+                }
+                // @ts-ignore
+                bookmarkWidget.addBookmark(highlight);
+                dismissHighlight();
+            },
+        },
+    ];
+    function handleClose() {
+        setOpen(false);
+    }
+    // coords
+    const mapCoords = (r) => {
+        const s = model.bpToPx({
+            refName: r.refName,
+            coord: r.start,
+        });
+        const e = model.bpToPx({
+            refName: r.refName,
+            coord: r.end,
+        });
+        return s && e
+            ? {
+                width: Math.max(Math.abs(e.offsetPx - s.offsetPx), 3),
+                left: Math.min(s.offsetPx, e.offsetPx) - model.offsetPx,
+            }
+            : undefined;
+    };
+    const asm = assemblyManager.get(highlight === null || highlight === void 0 ? void 0 : highlight.assemblyName);
+    const h = mapCoords({
+        ...highlight,
+        refName: (_c = asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(highlight.refName)) !== null && _c !== void 0 ? _c : highlight.refName,
+    });
+    return h ? (react_1.default.createElement("div", { className: classes.highlight, style: {
+            left: h.left,
+            width: h.width,
+        } },
+        react_1.default.createElement(material_1.Tooltip, { title: 'Highlighted from URL parameter', arrow: true },
+            react_1.default.createElement(material_1.IconButton, { ref: anchorEl, onClick: () => setOpen(true), style: { zIndex: 3 } },
+                react_1.default.createElement(Link_1.default, { fontSize: "small", sx: {
+                        color: `${(0, colord_1.colord)(color).darken(0.2).toRgbString()}`,
+                    } }))),
+        react_1.default.createElement(ui_1.Menu, { anchorEl: anchorEl.current, onMenuItemClick: (_event, callback) => {
+                callback(session);
+                handleClose();
+            }, open: open, onClose: handleClose, menuItems: menuItems }))) : null;
+});
+const HighlightGroup = (0, mobx_react_1.observer)(function HighlightGroup({ model, }) {
+    return model.highlight.map((highlight, idx) => (react_1.default.createElement(Highlight, { key: JSON.stringify(highlight) + '-' + idx, model: model, highlight: highlight })));
+});
+exports.default = HighlightGroup;

package/dist/LinearGenomeView/components/MiniControls.js

@@ -6,13 +6,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
+const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
+const mui_1 = require("tss-react/mui");
+const util_1 = require("@jbrowse/core/util");
 // icons
 const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
 const ZoomOut_1 = __importDefault(require("@mui/icons-material/ZoomOut"));
 const KeyboardArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardArrowDown"));
-const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
-const mui_1 = require("tss-react/mui");
-const util_1 = require("@jbrowse/core/util");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     background: {
         position: 'absolute',
@@ -21,22 +21,20 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         background: theme.palette.background.paper,
     },
     focusedBackground: {
-        background: theme.palette.secondary.light,
-        svg: {
-            fill: theme.palette.secondary.contrastText,
-        },
+        background: (0, material_1.alpha)(theme.palette.secondary.light, 0.2),
     },
 }));
 const MiniControls = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes, cx } = useStyles();
+    const { classes } = useStyles();
     const { id, bpPerPx, maxBpPerPx, minBpPerPx, scaleFactor, hideHeader } = model;
     const { focusedViewId } = (0, util_1.getSession)(model);
-    return hideHeader ? (react_1.default.createElement(material_1.Paper, { className: cx(classes.background, focusedViewId === id ? classes.focusedBackground : undefined) },
-        react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: model.menuItems() },
-            react_1.default.createElement(KeyboardArrowDown_1.default, { fontSize: "small" })),
-        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1 },
-            react_1.default.createElement(ZoomOut_1.default, { fontSize: "small" })),
-        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1 },
-            react_1.default.createElement(ZoomIn_1.default, { fontSize: "small" })))) : null;
+    return hideHeader ? (react_1.default.createElement(material_1.Paper, { className: classes.background },
+        react_1.default.createElement(material_1.Paper, { className: focusedViewId === id ? classes.focusedBackground : undefined },
+            react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: model.menuItems() },
+                react_1.default.createElement(KeyboardArrowDown_1.default, { fontSize: "small" })),
+            react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1 },
+                react_1.default.createElement(ZoomOut_1.default, { fontSize: "small" })),
+            react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1 },
+                react_1.default.createElement(ZoomIn_1.default, { fontSize: "small" }))))) : null;
 });
 exports.default = MiniControls;

package/dist/LinearGenomeView/components/OverviewHighlight.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
+import { LinearGenomeViewModel } from '../model';
+type LGV = LinearGenomeViewModel;
+declare const OverviewHighlight: ({ model, overview, }: {
+    model: LGV;
+    overview: Base1DViewModel;
+}) => React.JSX.Element[];
+export default OverviewHighlight;

package/dist/LinearGenomeView/components/OverviewHighlight.js

@@ -0,0 +1,62 @@
+"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 mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const colord_1 = require("@jbrowse/core/util/colord");
+const util_1 = require("@jbrowse/core/util");
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    var _a, _b, _c, _d, _e, _f;
+    return ({
+        highlight: {
+            height: '100%',
+            position: 'absolute',
+            background: `${(0, colord_1.colord)((_b = (_a = theme.palette.highlight) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod')
+                .alpha(0.35)
+                .toRgbString()}`,
+            borderLeft: `1px solid ${(_d = (_c = theme.palette.highlight) === null || _c === void 0 ? void 0 : _c.main) !== null && _d !== void 0 ? _d : 'goldenrod'}`,
+            borderRight: `1px solid ${(_f = (_e = theme.palette.highlight) === null || _e === void 0 ? void 0 : _e.main) !== null && _f !== void 0 ? _f : 'goldenrod'}`,
+        },
+    });
+});
+const OverviewHighlight = (0, mobx_react_1.observer)(function OverviewHighlight({ model, overview, }) {
+    const { classes } = useStyles();
+    const { cytobandOffset } = model;
+    const session = (0, util_1.getSession)(model);
+    const { assemblyManager } = session;
+    // coords
+    const mapCoords = (r) => {
+        const s = overview.bpToPx({
+            ...r,
+            coord: r.reversed ? r.end : r.start,
+        });
+        const e = overview.bpToPx({
+            ...r,
+            coord: r.reversed ? r.start : r.end,
+        });
+        return s !== undefined && e != undefined
+            ? {
+                width: Math.abs(e - s),
+                left: s + cytobandOffset,
+            }
+            : undefined;
+    };
+    return model.highlight
+        .map(h => {
+        var _a;
+        const asm = assemblyManager.get(h === null || h === void 0 ? void 0 : h.assemblyName);
+        return mapCoords({
+            ...h,
+            refName: (_a = asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(h.refName)) !== null && _a !== void 0 ? _a : h.refName,
+        });
+    })
+        .filter(util_1.notEmpty)
+        .map(({ left, width }, idx) => (react_1.default.createElement("div", { key: `${left}_${width}_${idx}`, className: classes.highlight, style: {
+            width: width,
+            left: left,
+        } })));
+});
+exports.default = OverviewHighlight;

package/dist/LinearGenomeView/components/OverviewRubberband.d.ts

@@ -5,6 +5,6 @@ type LGV = LinearGenomeViewModel;
 declare const OverviewRubberband: ({ model, overview, ControlComponent, }: {
     model: LGV;
     overview: Base1DViewModel;
-    ControlComponent?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    ControlComponent?: React.ReactElement;
 }) => React.JSX.Element;
 export default OverviewRubberband;

package/dist/LinearGenomeView/components/OverviewScalebar.js

@@ -41,6 +41,7 @@ const util_3 = require("./util");
 const OverviewRubberband_1 = __importDefault(require("./OverviewRubberband"));
 const Cytobands_1 = __importDefault(require("./Cytobands"));
 const OverviewScalebarPolygon_1 = __importDefault(require("./OverviewScalebarPolygon"));
+const OverviewHighlight_1 = __importDefault(require("./OverviewHighlight"));
 const wholeSeqSpacer = 2;
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     scalebar: {
@@ -145,6 +146,7 @@ const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview,
     const { classes } = useStyles();
     const theme = (0, material_1.useTheme)();
     const { dynamicBlocks, showCytobands, cytobandOffset } = model;
+    const { pluginManager } = (0, util_1.getEnv)(model);
     const visibleRegions = dynamicBlocks.contentBlocks;
     const overviewVisibleRegions = overview.dynamicBlocks;
     const { tertiary, primary } = theme.palette;
@@ -165,6 +167,7 @@ const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview,
     }) || 0;
     const color = showCytobands ? '#f00' : scalebarColor;
     const transparency = showCytobands ? 0.1 : 0.3;
+    const additional = pluginManager.evaluateExtensionPoint('LinearGenomeView-OverviewScalebarComponent', undefined, { model, overview });
     return (react_1.default.createElement("div", { className: classes.scalebar },
         react_1.default.createElement("div", { className: classes.scalebarVisibleRegion, style: {
                 width: lastOverviewPx - firstOverviewPx,
@@ -179,7 +182,9 @@ const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview,
                     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: `${JSON.stringify(block)}-${idx}` }));
-        })));
+        }),
+        react_1.default.createElement(OverviewHighlight_1.default, { model: model, overview: overview }),
+        additional));
 });
 const OverviewScalebar = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { classes } = useStyles();

package/dist/LinearGenomeView/components/OverviewScalebarPolygon.d.ts

@@ -4,6 +4,6 @@ import { LinearGenomeViewModel } from '..';
 declare const OverviewScalebarPolygon: ({ model, overview, useOffset, }: {
     model: LinearGenomeViewModel;
     overview: Base1DViewModel;
-    useOffset?: boolean | undefined;
+    useOffset?: boolean;
 }) => React.JSX.Element | null;
 export default OverviewScalebarPolygon;

package/dist/LinearGenomeView/components/RefNameAutocomplete/index.d.ts

@@ -4,15 +4,15 @@ import { TextFieldProps as TFP } from '@mui/material';
 import { LinearGenomeViewModel } from '../../model';
 declare const RefNameAutocomplete: ({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp, minWidth, maxWidth, TextFieldProps, }: {
     model: LinearGenomeViewModel;
-    onSelect?: ((region: BaseResult) => void) | undefined;
-    onChange?: ((val: string) => void) | undefined;
-    assemblyName?: string | undefined;
-    value?: string | undefined;
+    onSelect?: (region: BaseResult) => void;
+    onChange?: (val: string) => void;
+    assemblyName?: string;
+    value?: string;
     fetchResults: (query: string) => Promise<BaseResult[]>;
-    style?: React.CSSProperties | undefined;
-    minWidth?: number | undefined;
-    maxWidth?: number | undefined;
-    showHelp?: boolean | undefined;
-    TextFieldProps?: TFP | undefined;
+    style?: React.CSSProperties;
+    minWidth?: number;
+    maxWidth?: number;
+    showHelp?: boolean;
+    TextFieldProps?: TFP;
 }) => React.JSX.Element;
 export default RefNameAutocomplete;

package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js

@@ -45,7 +45,8 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
     const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
     const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
     (0, react_1.useEffect)(() => {
-        let active = true;
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
         (async () => {
             try {
                 if (debouncedSearch === '' || !assemblyName) {
@@ -53,21 +54,14 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
                 }
                 setLoaded(false);
                 const results = await fetchResults(debouncedSearch);
-                if (active) {
-                    setLoaded(true);
-                    setSearchOptions((0, util_2.getDeduplicatedResult)(results));
-                }
+                setLoaded(true);
+                setSearchOptions((0, util_2.getDeduplicatedResult)(results));
             }
             catch (e) {
                 console.error(e);
-                if (active) {
-                    session.notify(`${e}`, 'error');
-                }
+                session.notifyError(`${e}`, e);
             }
         })();
-        return () => {
-            active = false;
-        };
     }, [assemblyName, fetchResults, debouncedSearch, session, model]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     // heuristic, text width + 60 accommodates help icon and search icon
@@ -82,29 +76,28 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
     }))) || [], [regions]);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
-                setInputValue(newInputValue);
-                onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
-            }, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
-                setOpen(false);
-                setLoaded(true);
-                if (hasDisplayedRegions) {
-                    setCurrentSearch('');
-                    setSearchOptions(undefined);
-                }
-            }, onChange: (_event, selectedOption) => {
-                if (!selectedOption || !assemblyName) {
-                    return;
-                }
-                if (typeof selectedOption === 'string') {
-                    // handles string inputs on keyPress enter
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({ label: selectedOption }));
-                }
-                else {
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
-                }
-                setInputValue(inputBoxVal);
-            }, options: (searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? searchOptions : regionOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => (0, util_2.getFiltered)(opts, inputValue), renderInput: params => (react_1.default.createElement(AutocompleteTextField_1.default, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
+    return (react_1.default.createElement(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
+            setInputValue(newInputValue);
+            onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
+        }, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
+            setOpen(false);
+            setLoaded(true);
+            if (hasDisplayedRegions) {
+                setCurrentSearch('');
+                setSearchOptions(undefined);
+            }
+        }, onChange: (_event, selectedOption) => {
+            if (!selectedOption || !assemblyName) {
+                return;
+            }
+            if (typeof selectedOption === 'string') {
+                // handles string inputs on keyPress enter
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({ label: selectedOption }));
+            }
+            else {
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
+            }
+            setInputValue(inputBoxVal);
+        }, options: (searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? searchOptions : regionOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => (0, util_2.getFiltered)(opts, inputValue), renderInput: params => (react_1.default.createElement(AutocompleteTextField_1.default, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() }));
 });
 exports.default = RefNameAutocomplete;

package/dist/LinearGenomeView/components/Rubberband.d.ts

@@ -3,6 +3,6 @@ import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare const Rubberband: ({ model, ControlComponent, }: {
     model: LGV;
-    ControlComponent?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    ControlComponent?: React.ReactElement;
 }) => React.JSX.Element;
 export default Rubberband;

package/dist/LinearGenomeView/components/SearchBox.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
 import { LinearGenomeViewModel } from '..';
 declare const SearchBox: ({ model, showHelp, }: {
-    showHelp?: boolean | undefined;
+    showHelp?: boolean;
     model: LinearGenomeViewModel;
 }) => React.JSX.Element;
 export default SearchBox;

package/dist/LinearGenomeView/components/SearchResultsTable.js

@@ -74,7 +74,7 @@ function SearchResultsTable({ searchResults, assemblyName: optAssemblyName, mode
                             }
                             catch (e) {
                                 console.error(e);
-                                session.notify(`${e}`, 'error');
+                                session.notifyError(`${e}`, e);
                             }
                             handleClose();
                         }, color: "primary", variant: "contained" }, "Go")))))))));

package/dist/LinearGenomeView/components/TrackContainer.js

@@ -33,7 +33,6 @@ const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const react_error_boundary_1 = require("react-error-boundary");
 const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
 const TrackLabelContainer_1 = __importDefault(require("./TrackLabelContainer"));
 const TrackRenderingContainer_1 = __importDefault(require("./TrackRenderingContainer"));
 const useStyles = (0, mui_1.makeStyles)()({
@@ -46,40 +45,28 @@ const useStyles = (0, mui_1.makeStyles)()({
         position: 'relative',
         zIndex: 2,
     },
-    overlay: {
-        pointerEvents: 'none',
-        position: 'absolute',
-        top: 0,
-        left: 0,
-        width: '100%',
-        zIndex: 3,
-    },
 });
 const TrackContainer = (0, mobx_react_1.observer)(function ({ model, track, }) {
     const { classes } = useStyles();
     const display = track.displays[0];
     const { draggingTrackId } = model;
-    const ref2 = (0, react_1.useRef)(null);
-    const dimmed = draggingTrackId !== undefined && draggingTrackId !== display.id;
-    const debouncedOnDragEnter = (0, util_1.useDebouncedCallback)(() => {
-        if ((0, mobx_state_tree_1.isAlive)(display) && dimmed) {
-            model.moveTrack(draggingTrackId, track.id);
-        }
-    }, 100);
-    return (react_1.default.createElement(material_1.Paper, { ref: ref2, className: classes.root, variant: "outlined", onClick: event => {
+    const ref = (0, react_1.useRef)(null);
+    return (react_1.default.createElement(material_1.Paper, { ref: ref, className: classes.root, variant: "outlined", onClick: event => {
             var _a;
             if (event.detail === 2 && !track.displays[0].featureIdUnderMouse) {
-                const left = ((_a = ref2.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;
+                const left = ((_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;
                 model.zoomTo(model.bpPerPx / 2, event.clientX - left, true);
             }
         } },
         react_1.default.createElement(TrackLabelContainer_1.default, { track: track, view: model }),
         react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: e => react_1.default.createElement(ui_1.ErrorMessage, { error: e.error }) },
-            react_1.default.createElement(TrackRenderingContainer_1.default, { model: model, track: track, onDragEnter: debouncedOnDragEnter })),
-        react_1.default.createElement("div", { className: classes.overlay, style: {
-                height: display.height,
-                background: dimmed ? 'rgba(0, 0, 0, 0.4)' : undefined,
-            }, onDragEnter: debouncedOnDragEnter }),
+            react_1.default.createElement(TrackRenderingContainer_1.default, { model: model, track: track, onDragEnter: () => {
+                    if ((0, mobx_state_tree_1.isAlive)(display) &&
+                        draggingTrackId !== undefined &&
+                        draggingTrackId !== display.id) {
+                        model.moveTrack(draggingTrackId, track.id);
+                    }
+                } })),
         react_1.default.createElement(ui_1.ResizeHandle, { onDrag: display.resizeHeight, className: classes.resizeHandle })));
 });
 exports.default = TrackContainer;

package/dist/LinearGenomeView/components/TrackLabel.js

@@ -17,6 +17,10 @@ const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
 const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const Minimize_1 = __importDefault(require("@mui/icons-material/Minimize"));
 const Add_1 = __importDefault(require("@mui/icons-material/Add"));
+const KeyboardDoubleArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowDown"));
+const KeyboardDoubleArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowUp"));
+const KeyboardArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardArrowDown"));
+const KeyboardArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardArrowUp"));
 const TrackLabelDragHandle_1 = __importDefault(require("./TrackLabelDragHandle"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     root: {
@@ -24,9 +28,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         '&:hover': {
             background: theme.palette.background.paper,
         },
-        transition: theme.transitions.create(['background'], {
-            duration: theme.transitions.duration.shortest,
-        }),
     },
     trackName: {
         margin: '0 auto',
@@ -49,9 +50,35 @@ const TrackLabel = (0, mobx_react_1.observer)(react_1.default.forwardRef(functio
     const trackName = (0, tracks_1.getTrackName)(trackConf, session);
     const items = [
         {
-            label: minimized ? 'Restore track' : 'Minimize track',
-            icon: minimized ? Add_1.default : Minimize_1.default,
-            onClick: () => track.setMinimized(!minimized),
+            label: 'Track order',
+            type: 'subMenu',
+            subMenu: [
+                {
+                    label: minimized ? 'Restore track' : 'Minimize track',
+                    icon: minimized ? Add_1.default : Minimize_1.default,
+                    onClick: () => track.setMinimized(!minimized),
+                },
+                {
+                    label: 'Move track to top',
+                    icon: KeyboardDoubleArrowUp_1.default,
+                    onClick: () => view.moveTrackToTop(track.id),
+                },
+                {
+                    label: 'Move track up',
+                    icon: KeyboardArrowUp_1.default,
+                    onClick: () => view.moveTrackUp(track.id),
+                },
+                {
+                    label: 'Move track down',
+                    icon: KeyboardArrowDown_1.default,
+                    onClick: () => view.moveTrackDown(track.id),
+                },
+                {
+                    label: 'Move track to bottom',
+                    icon: KeyboardDoubleArrowDown_1.default,
+                    onClick: () => view.moveTrackToBottom(track.id),
+                },
+            ],
         },
         ...(((_a = session.getTrackActionMenuItems) === null || _a === void 0 ? void 0 : _a.call(session, trackConf)) || []),
         ...track.trackMenuItems(),

package/dist/LinearGenomeView/components/TracksContainer.js

@@ -41,6 +41,7 @@ const Gridlines_1 = __importDefault(require("./Gridlines"));
 const CenterLine_1 = __importDefault(require("./CenterLine"));
 const VerticalGuide_1 = __importDefault(require("./VerticalGuide"));
 const RubberbandSpan_1 = __importDefault(require("./RubberbandSpan"));
+const Highlight_1 = __importDefault(require("./Highlight"));
 const useStyles = (0, mui_1.makeStyles)()({
     tracksContainer: {
         position: 'relative',
@@ -67,6 +68,7 @@ const TracksContainer = (0, mobx_react_1.observer)(function TracksContainer({ ch
                 top: anchorPosition.clientY,
             }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null,
         react_1.default.createElement(Rubberband_1.default, { model: model, ControlComponent: react_1.default.createElement(Scalebar_1.default, { model: model, style: { height: __1.SCALE_BAR_HEIGHT, boxSizing: 'border-box' } }) }),
+        react_1.default.createElement(Highlight_1.default, { model: model }),
         additional,
         children));
 });

package/dist/LinearGenomeView/components/ZoomControls.js

@@ -45,16 +45,16 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
 }));
 const ZoomControls = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
-    const { maxBpPerPx, minBpPerPx, bpPerPx, scaleFactor } = model;
+    const { maxBpPerPx, minBpPerPx, bpPerPx } = model;
     const [value, setValue] = (0, react_1.useState)(-Math.log2(bpPerPx) * 100);
     (0, react_1.useEffect)(() => {
         setValue(-Math.log2(bpPerPx) * 100);
     }, [setValue, bpPerPx]);
     return (react_1.default.createElement("div", { className: classes.container },
-        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, size: "large" },
+        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001, size: "large" },
             react_1.default.createElement(ZoomOut_1.default, null)),
-        react_1.default.createElement(material_1.Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: (_, val) => setValue(val), onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), disabled: scaleFactor !== 1 }),
-        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, size: "large" },
+        react_1.default.createElement(material_1.Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: (_, val) => setValue(val), onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)) }),
+        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001, size: "large" },
             react_1.default.createElement(ZoomIn_1.default, null))));
 });
 exports.default = ZoomControls;