@jbrowse/plugin-linear-genome-view 2.9.0 → 2.10.1

package/dist/LinearGenomeView/components/OverviewScalebarPolygon.js

@@ -0,0 +1,46 @@
+"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 mobx_react_1 = require("mobx-react");
+// locals
+const __1 = require("..");
+const OverviewScalebarPolygon = (0, mobx_react_1.observer)(function ({ 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;
+    // catches possible null from at's below
+    if (!contentBlocks.length) {
+        return null;
+    }
+    const first = contentBlocks.at(0);
+    const last = contentBlocks.at(-1);
+    const topLeft = (overview.bpToPx({
+        ...first,
+        coord: first.reversed ? first.end : first.start,
+    }) || 0) +
+        cytobandOffset * multiplier;
+    const topRight = (overview.bpToPx({
+        ...last,
+        coord: last.reversed ? last.start : last.end,
+    }) || 0) +
+        cytobandOffset * multiplier;
+    const startPx = Math.max(0, -offsetPx);
+    const endPx = startPx +
+        totalWidthPxWithoutBorders +
+        (contentBlocks.length * interRegionPaddingWidth) / 2;
+    const points = [
+        [startPx, __1.HEADER_BAR_HEIGHT],
+        [endPx, __1.HEADER_BAR_HEIGHT],
+        [topRight, 0],
+        [topLeft, 0],
+    ];
+    return (react_1.default.createElement("polygon", { points: points.toString(), fill: (0, material_1.alpha)(polygonColor, 0.3), stroke: (0, material_1.alpha)(polygonColor, 0.8) }));
+});
+exports.default = OverviewScalebarPolygon;

package/dist/LinearGenomeView/components/TracksContainer.js

@@ -30,6 +30,7 @@ const react_1 = __importStar(require("react"));
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
 // local utils
 const __1 = require("..");
 const hooks_1 = require("./hooks");
@@ -40,7 +41,6 @@ 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 util_1 = require("@jbrowse/core/util");
 const useStyles = (0, mui_1.makeStyles)()({
     tracksContainer: {
         position: 'relative',

package/dist/LinearGenomeView/model.d.ts

@@ -21,7 +21,9 @@ export interface BpOffset {
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     filename?: string;
-    Wrapper?: React.FC<any>;
+    Wrapper?: React.FC<{
+        children: React.ReactNode;
+    }>;
     fontSize?: number;
     rulerHeight?: number;
     textHeight?: number;
@@ -47,6 +49,9 @@ export declare const WIDGET_HEIGHT = 32;
 /**
  * #stateModel LinearGenomeView
  * #category view
+ *
+ * extends
+ * - [BaseViewModel](../baseviewmodel)
  */
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;

package/dist/LinearGenomeView/model.js

@@ -83,6 +83,9 @@ exports.WIDGET_HEIGHT = 32;
 /**
  * #stateModel LinearGenomeView
  * #category view
+ *
+ * extends
+ * - [BaseViewModel](../baseviewmodel)
  */
 function stateModelFactory(pluginManager) {
     return mobx_state_tree_1.types

package/dist/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -10,9 +10,9 @@ const material_1 = require("@mui/material");
 // locals
 const __1 = require("..");
 const Cytobands_1 = __importDefault(require("../components/Cytobands"));
-const OverviewScalebar_1 = require("../components/OverviewScalebar");
 const SVGRuler_1 = __importDefault(require("./SVGRuler"));
 const SVGScalebar_1 = __importDefault(require("./SVGScalebar"));
+const OverviewScalebarPolygon_1 = __importDefault(require("../components/OverviewScalebarPolygon"));
 function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
     const { width, assemblyNames, showCytobands, displayedRegions } = model;
     const { assemblyManager } = (0, util_1.getSession)(model);
@@ -49,7 +49,7 @@ function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
             react_1.default.createElement(Cytobands_1.default, { overview: overview, assembly: assembly, block: block }),
             react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
             react_1.default.createElement("g", { transform: `translate(0,${__1.HEADER_OVERVIEW_HEIGHT})` },
-                react_1.default.createElement(OverviewScalebar_1.Polygon, { overview: overview, model: model, useOffset: false })))) : null,
+                react_1.default.createElement(OverviewScalebarPolygon_1.default, { overview: overview, model: model, useOffset: false })))) : null,
         react_1.default.createElement("g", { transform: `translate(0 ${fontSize + y})` },
             react_1.default.createElement(SVGScalebar_1.default, { model: model, fontSize: fontSize })),
         react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight + y})` },

package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.d.ts

@@ -1,12 +1,5 @@
 import { LinearGenomeViewModel, ExportSvgOptions } from '..';
 type LGV = LinearGenomeViewModel;
-interface Display {
-    height: number;
-}
-interface Track {
-    displays: Display[];
-}
-export declare function totalHeight(tracks: Track[], textHeight: number, trackLabels: string): number;
 export declare function renderToSvg(model: LGV, opts: ExportSvgOptions): Promise<string>;
 export { default as SVGRuler } from './SVGRuler';
 export { default as SVGTracks } from './SVGTracks';

package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js

@@ -3,35 +3,33 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SVGTracks = exports.SVGRuler = exports.renderToSvg = exports.totalHeight = void 0;
+exports.SVGTracks = exports.SVGRuler = exports.renderToSvg = void 0;
 /* eslint-disable react-refresh/only-export-components */
 const react_1 = __importDefault(require("react"));
-const server_1 = require("react-dom/server");
 const mobx_1 = require("mobx");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const SVGBackground_1 = __importDefault(require("./SVGBackground"));
 const SVGTracks_1 = __importDefault(require("./SVGTracks"));
 const SVGHeader_1 = __importDefault(require("./SVGHeader"));
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function totalHeight(tracks, textHeight, trackLabels) {
-    return (0, util_1.sum)(tracks.map(t => t.displays[0].height +
-        (['none', 'left'].includes(trackLabels) ? 0 : textHeight)));
-}
-exports.totalHeight = totalHeight;
+const util_2 = require("./util");
 // render LGV to SVG
 async function renderToSvg(model, opts) {
-    var _a;
     await (0, mobx_1.when)(() => model.initialized);
     const { textHeight = 18, headerHeight = 40, rulerHeight = 50, fontSize = 13, cytobandHeight = 100, trackLabels = 'offset', themeName = 'default', Wrapper = ({ children }) => react_1.default.createElement(react_1.default.Fragment, null, children), } = opts;
     const session = (0, util_1.getSession)(model);
-    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const { allThemes } = session;
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const { createRootFn } = (0, mobx_state_tree_1.getRoot)(model);
+    const theme = allThemes === null || allThemes === void 0 ? void 0 : allThemes()[themeName];
     const { width, tracks, showCytobands } = model;
     const shift = 50;
     const c = +showCytobands * cytobandHeight;
     const offset = headerHeight + rulerHeight + c + 10;
-    const height = totalHeight(tracks, textHeight, trackLabels) + offset + 100;
+    const height = (0, util_2.totalHeight)(tracks, textHeight, trackLabels) + offset + 100;
     const displayResults = await Promise.all(tracks.map(async (track) => {
         const display = track.displays[0];
         await (0, mobx_1.when)(() => !display.renderProps().notReady);
@@ -41,14 +39,14 @@ async function renderToSvg(model, opts) {
     const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
     const w = width + trackLabelOffset;
     // the xlink namespace is used for rendering <image> tag
-    return (0, server_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: (0, ui_1.createJBrowseTheme)(theme) },
+    return (0, util_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: (0, ui_1.createJBrowseTheme)(theme) },
         react_1.default.createElement(Wrapper, null,
             react_1.default.createElement("svg", { width: w, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, height].toString() },
                 react_1.default.createElement(SVGBackground_1.default, { width: w, height: height, shift: shift }),
                 react_1.default.createElement("g", { transform: `translate(${shift} 0)` },
                     react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
                         react_1.default.createElement(SVGHeader_1.default, { model: model, fontSize: fontSize, rulerHeight: rulerHeight, cytobandHeight: cytobandHeight })),
-                    react_1.default.createElement(SVGTracks_1.default, { textHeight: textHeight, fontSize: fontSize, model: model, displayResults: displayResults, offset: offset, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset }))))));
+                    react_1.default.createElement(SVGTracks_1.default, { textHeight: textHeight, fontSize: fontSize, model: model, displayResults: displayResults, offset: offset, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset }))))), createRootFn);
 }
 exports.renderToSvg = renderToSvg;
 var SVGRuler_1 = require("./SVGRuler");

package/dist/LinearGenomeView/svgcomponents/util.d.ts

@@ -0,0 +1,8 @@
+interface Display {
+    height: number;
+}
+interface Track {
+    displays: Display[];
+}
+export declare function totalHeight(tracks: Track[], textHeight: number, trackLabels: string): number;
+export {};

package/dist/LinearGenomeView/svgcomponents/util.js

@@ -0,0 +1,9 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.totalHeight = void 0;
+const util_1 = require("@jbrowse/core/util");
+function totalHeight(tracks, textHeight, trackLabels) {
+    return (0, util_1.sum)(tracks.map(t => t.displays[0].height +
+        (['none', 'left'].includes(trackLabels) ? 0 : textHeight)));
+}
+exports.totalHeight = totalHeight;

package/dist/index.d.ts

@@ -1080,11 +1080,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -1136,11 +1142,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -1387,11 +1399,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -1443,11 +1461,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -1704,11 +1728,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -1760,11 +1790,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -2011,11 +2047,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -2067,11 +2109,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -2328,11 +2376,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -2384,11 +2438,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -2635,11 +2695,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -2691,11 +2757,17 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         load(): Promise<void>;
                         loadPre(): Promise<void>;
                     } & {
-                        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getAdapterMapEntry(adapterConf: {
+                            [x: string]: unknown;
+                        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                        getRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
-                        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                        getReverseRefNameMapForAdapter(adapterConf: {
+                            [x: string]: unknown;
+                        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                             [x: string]: string | undefined;
                         }>;
                     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -2761,5 +2833,6 @@ export type { ExportSvgDisplayOptions, BaseLinearDisplayModel, BlockModel, } fro
 export { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay';
 export { baseLinearDisplayConfigSchema, BaseLinearDisplay, BlockMsg, BaseLinearDisplayComponent, TrackHeightMixin, FeatureDensityMixin, TooLargeMessage, } from './BaseLinearDisplay';
 export { type LinearGenomeViewModel, type LinearGenomeViewStateModel, RefNameAutocomplete, SearchBox, } from './LinearGenomeView';
-export { renderToSvg, SVGTracks, totalHeight, SVGRuler, } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView';
+export { renderToSvg, SVGTracks, SVGRuler, } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView';
+export { totalHeight } from './LinearGenomeView/svgcomponents/util';
 export { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory, } from './LinearBasicDisplay';

package/dist/index.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.SVGRuler = exports.totalHeight = exports.SVGTracks = exports.renderToSvg = exports.SearchBox = exports.RefNameAutocomplete = exports.TooLargeMessage = exports.FeatureDensityMixin = exports.TrackHeightMixin = exports.BaseLinearDisplayComponent = exports.BlockMsg = exports.BaseLinearDisplay = exports.baseLinearDisplayConfigSchema = exports.linearBareDisplayConfigSchemaFactory = void 0;
+exports.linearBasicDisplayModelFactory = exports.linearBasicDisplayConfigSchemaFactory = exports.totalHeight = exports.SVGRuler = exports.SVGTracks = exports.renderToSvg = exports.SearchBox = exports.RefNameAutocomplete = exports.TooLargeMessage = exports.FeatureDensityMixin = exports.TrackHeightMixin = exports.BaseLinearDisplayComponent = exports.BlockMsg = exports.BaseLinearDisplay = exports.baseLinearDisplayConfigSchema = exports.linearBareDisplayConfigSchemaFactory = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
@@ -108,8 +108,9 @@ Object.defineProperty(exports, "SearchBox", { enumerable: true, get: function ()
 var SVGLinearGenomeView_1 = require("./LinearGenomeView/svgcomponents/SVGLinearGenomeView");
 Object.defineProperty(exports, "renderToSvg", { enumerable: true, get: function () { return SVGLinearGenomeView_1.renderToSvg; } });
 Object.defineProperty(exports, "SVGTracks", { enumerable: true, get: function () { return SVGLinearGenomeView_1.SVGTracks; } });
-Object.defineProperty(exports, "totalHeight", { enumerable: true, get: function () { return SVGLinearGenomeView_1.totalHeight; } });
 Object.defineProperty(exports, "SVGRuler", { enumerable: true, get: function () { return SVGLinearGenomeView_1.SVGRuler; } });
+var util_2 = require("./LinearGenomeView/svgcomponents/util");
+Object.defineProperty(exports, "totalHeight", { enumerable: true, get: function () { return util_2.totalHeight; } });
 var LinearBasicDisplay_2 = require("./LinearBasicDisplay");
 Object.defineProperty(exports, "linearBasicDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearBasicDisplay_2.configSchema; } });
 Object.defineProperty(exports, "linearBasicDisplayModelFactory", { enumerable: true, get: function () { return LinearBasicDisplay_2.modelFactory; } });

package/esm/BaseLinearDisplay/components/Tooltip.js

@@ -1,10 +1,10 @@
-import React, { useState, useMemo } from 'react';
+import React from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { SanitizedHTML } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { Portal, alpha } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import { usePopper } from 'react-popper';
+import { useClientPoint, useFloating, useInteractions, } from '@floating-ui/react';
 function round(value) {
     return Math.round(value * 1e5) / 1e5;
 }
@@ -27,39 +27,27 @@ const useStyles = makeStyles()(theme => ({
 const TooltipContents = React.forwardRef(function TooltipContents2({ message }, ref) {
     return (React.createElement("div", { ref: ref }, React.isValidElement(message) ? (message) : message ? (React.createElement(SanitizedHTML, { html: String(message) })) : null));
 });
-const Tooltip = observer(({ model, clientMouseCoord, }) => {
+const Tooltip = observer(function ({ model, clientMouseCoord, }) {
     var _a, _b;
     const { theme, classes } = useStyles();
     const { featureUnderMouse } = model;
-    const [width, setWidth] = useState(0);
-    const [popperElt, setPopperElt] = useState(null);
-    // must be memoized a la https://github.com/popperjs/react-popper/issues/391
-    const virtElement = useMemo(() => ({
-        getBoundingClientRect: () => {
-            const x = clientMouseCoord[0] + width / 2 + 20;
-            const y = clientMouseCoord[1];
-            return {
-                top: y,
-                left: x,
-                bottom: y,
-                right: x,
-                width: 0,
-                height: 0,
-                x,
-                y,
-                toJSON() { },
-            };
-        },
-    }), [clientMouseCoord, width]);
-    const { styles, attributes } = usePopper(virtElement, popperElt);
+    const x = clientMouseCoord[0] + 15;
+    const y = clientMouseCoord[1];
+    const { refs, floatingStyles, context } = useFloating({
+        placement: 'right',
+    });
+    const clientPoint = useClientPoint(context, { x, y });
+    const { getFloatingProps } = useInteractions([clientPoint]);
     const contents = featureUnderMouse
         ? getConf(model, 'mouseover', { feature: featureUnderMouse })
         : undefined;
     const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
     return featureUnderMouse && contents ? (React.createElement(Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
-        React.createElement("div", { ref: setPopperElt, className: classes.tooltip, 
-            // zIndex needed to go over widget drawer
-            style: { ...styles.popper, zIndex: 100000 }, ...attributes.popper },
-            React.createElement(TooltipContents, { ref: elt => setWidth((elt === null || elt === void 0 ? void 0 : elt.getBoundingClientRect().width) || 0), message: contents })))) : null;
+        React.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
+                ...floatingStyles,
+                zIndex: 100000,
+                pointerEvents: 'none',
+            }, ...getFloatingProps() },
+            React.createElement(TooltipContents, { message: contents })))) : null;
 });
 export default Tooltip;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -69,11 +69,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, Feature>; /**
-             * #getter
-             * a CompositeMap of `featureId -> feature obj` that
-             * just looks in all the block data for that feature
-             */
+            features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -132,9 +128,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined; /**
-         * #property
-         */
+        blockState?: Record<string, any> | undefined;
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -142,9 +136,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
-             * #getter
-             */
+            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -361,11 +353,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
-            features: Map<string, Feature>; /**
-             * #getter
-             * a CompositeMap of `featureId -> feature obj` that
-             * just looks in all the block data for that feature
-             */
+            features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;