@jbrowse/plugin-variants 3.2.0 → 3.3.0

package/dist/MultiLinearVariantDisplay/components/VariantDisplayComponent.js

@@ -7,8 +7,8 @@ const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_react_1 = require("mobx-react");
-const Crosshair_1 = __importDefault(require("./Crosshair"));
-const LegendBar_1 = __importDefault(require("../../shared/components/LegendBar"));
+const MultiVariantCrosshairs_1 = __importDefault(require("../../shared/components/MultiVariantCrosshairs"));
+const MultiVariantLegendBar_1 = __importDefault(require("../../shared/components/MultiVariantLegendBar"));
 const MultiLinearVariantDisplayComponent = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const ref = (0, react_1.useRef)(null);
@@ -24,6 +24,6 @@ const MultiLinearVariantDisplayComponent = (0, mobx_react_1.observer)(function (
         }, onMouseLeave: () => {
             setMouseY(undefined);
             setMouseX(undefined);
-        }, children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }), (0, jsx_runtime_1.jsx)(LegendBar_1.default, { model: model }), mouseX && mouseY ? ((0, jsx_runtime_1.jsx)(Crosshair_1.default, { mouseX: mouseX, mouseY: mouseY, model: model })) : null] }));
+        }, children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }), (0, jsx_runtime_1.jsx)(MultiVariantLegendBar_1.default, { model: model }), mouseX && mouseY ? ((0, jsx_runtime_1.jsx)(MultiVariantCrosshairs_1.default, { mouseX: mouseX, mouseY: mouseY, model: model })) : null] }));
 });
 exports.default = MultiLinearVariantDisplayComponent;

package/dist/MultiLinearVariantDisplay/index.js

@@ -46,7 +46,7 @@ function MultiLinearVariantDisplayF(pluginManager) {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'MultiLinearVariantDisplay',
-            displayName: 'Multi-variant display (regular)',
+            displayName: 'Multi-sample variant display (regular)',
             configSchema,
             stateModel: (0, model_1.default)(configSchema),
             trackType: 'VariantTrack',

package/dist/MultiLinearVariantDisplay/model.d.ts

@@ -89,11 +89,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    lengthCutoffFilter: import("mobx-state-tree").IType<number | undefined, number, number>;
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
+    referenceDrawingMode: import("mobx-state-tree").IType<string | undefined, string, string>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"MultiLinearVariantDisplay">;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -237,19 +239,28 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
 } & {
     sourcesLoadingStopToken: string | undefined;
+    simplifiedFeaturesStopToken: string | undefined;
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
     sourcesVolatile: import("../shared/types").Source[] | undefined;
     featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
     hasPhased: boolean;
     sampleInfo: undefined | Record<string, import("../shared/types").SampleInfo>;
-    hoveredGenotype: string | undefined;
+    hoveredGenotype: {
+        genotype: string;
+        name: string;
+    } | undefined;
 } & {
+    setJexlFilters(f?: string[]): void;
     setRowHeight(arg: number): void;
-    setHoveredGenotype(arg: string): void;
+    setHoveredGenotype(arg?: {
+        genotype: string;
+        name: string;
+    }): void;
     setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
     setLayout(layout: import("../shared/types").Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
+    setSimplifiedFeaturesLoading(str: string): void;
     setSources(sources: import("../shared/types").Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
@@ -257,7 +268,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     setAutoHeight(arg: boolean): void;
     setHasPhased(arg: boolean): void;
     setSampleInfo(arg: Record<string, import("../shared/types").SampleInfo>): void;
+    setReferenceDrawingMode(arg: string): void;
 } & {
+    readonly activeFilters: any;
     readonly preSources: import("../shared/types").Source[] | undefined;
     readonly sourcesWithoutLayout: {
         label: string;
@@ -278,6 +291,17 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         HP?: number;
     }[] | undefined;
 } & {
+    readonly sourceMap: {
+        [k: string]: {
+            label: string;
+            id: string;
+            baseUri?: string;
+            name: string;
+            color?: string;
+            group?: string;
+            HP?: number;
+        };
+    } | undefined;
     readonly rowHeight: number;
     adapterProps(): any;
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
@@ -331,6 +355,18 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         type?: undefined;
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        type: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        icon?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {

package/dist/MultiLinearVariantDisplay/model.js

@@ -46,7 +46,6 @@ function stateModelFactory(configSchema) {
         type: mobx_state_tree_1.types.literal('MultiLinearVariantDisplay'),
         rowHeightSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 11),
         minorAlleleFrequencyFilter: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-        autoHeight: false,
     }))
         .views(() => ({
         get rendererTypeName() {

package/dist/MultiLinearVariantDisplay/renderSvg.js

@@ -7,9 +7,9 @@ exports.renderSvg = renderSvg;
 const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
-const LegendBar_1 = __importDefault(require("../shared/components/LegendBar"));
+const MultiVariantLegendBar_1 = __importDefault(require("../shared/components/MultiVariantLegendBar"));
 async function renderSvg(self, opts, superRenderSvg) {
     await (0, mobx_1.when)(() => !!self.regionCannotBeRenderedText);
     const { offsetPx } = (0, util_1.getContainingView)(self);
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("g", { children: await superRenderSvg(opts) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: (0, jsx_runtime_1.jsx)(LegendBar_1.default, { model: self, orientation: "left", exportSVG: true }) })] }));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("g", { children: await superRenderSvg(opts) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: (0, jsx_runtime_1.jsx)(MultiVariantLegendBar_1.default, { model: self, orientation: "left", exportSVG: true }) })] }));
 }

package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js

@@ -1,8 +1,12 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
+const BaseTooltip_1 = __importDefault(require("@jbrowse/core/ui/BaseTooltip"));
 const util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
@@ -37,15 +41,21 @@ const LinesConnectingMatrixToGenomicPosition = (0, mobx_react_1.observer)(functi
     const assembly = assemblyManager.get(assemblyNames[0]);
     const b0 = ((_a = dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.widthPx) || 0;
     const w = b0 / ((featuresVolatile === null || featuresVolatile === void 0 ? void 0 : featuresVolatile.length) || 1);
-    return assembly && featuresVolatile ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(Wrapper, { exportSVG: exportSVG, model: model, children: [(0, jsx_runtime_1.jsx)(AllLines, { model: model, setMouseOverLine: setMouseOverLine }), mouseOverLine ? ((0, jsx_runtime_1.jsx)("line", { stroke: "#f00c", strokeWidth: 2, style: {
-                            pointerEvents: 'none',
-                        }, x1: mouseOverLine.idx * w + w / 2, x2: mouseOverLine.c, y1: lineZoneHeight, y2: 0, onMouseLeave: () => {
-                            setMouseOverLine(undefined);
-                        } })) : null] }), !exportSVG ? ((0, jsx_runtime_1.jsx)(ui_1.ResizeHandle, { style: {
+    return assembly && featuresVolatile ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(Wrapper, { exportSVG: exportSVG, model: model, children: [(0, jsx_runtime_1.jsx)(AllLines, { model: model, setMouseOverLine: setMouseOverLine }), mouseOverLine ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("line", { stroke: "#f00c", strokeWidth: 2, style: {
+                                    pointerEvents: 'none',
+                                }, x1: mouseOverLine.idx * w + w / 2, x2: mouseOverLine.c, y1: lineZoneHeight, y2: 0, onMouseLeave: () => {
+                                    setMouseOverLine(undefined);
+                                } }), (0, jsx_runtime_1.jsx)(LineTooltip, { contents: mouseOverLine.f.get('name') })] })) : null] }), !exportSVG ? ((0, jsx_runtime_1.jsx)(ui_1.ResizeHandle, { style: {
                     position: 'absolute',
                     top: lineZoneHeight - 4,
                 }, onDrag: n => model.setLineZoneHeight(lineZoneHeight + n), className: classes.resizeHandle })) : null] })) : null;
 });
+const TooltipContents = (0, react_1.forwardRef)(function TooltipContents2({ message }, ref) {
+    return ((0, jsx_runtime_1.jsx)("div", { ref: ref, children: (0, react_1.isValidElement)(message) ? (message) : message ? ((0, jsx_runtime_1.jsx)(ui_1.SanitizedHTML, { html: String(message) })) : null }));
+});
+const LineTooltip = (0, mobx_react_1.observer)(function ({ contents }) {
+    return contents ? ((0, jsx_runtime_1.jsx)(BaseTooltip_1.default, { children: (0, jsx_runtime_1.jsx)(TooltipContents, { message: contents }) })) : null;
+});
 const AllLines = (0, mobx_react_1.observer)(function ({ model, setMouseOverLine, }) {
     var _a;
     const { assemblyManager } = (0, util_1.getSession)(model);

package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js

@@ -7,9 +7,9 @@ const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_react_1 = require("mobx-react");
-const Crosshair_1 = __importDefault(require("./Crosshair"));
 const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./LinesConnectingMatrixToGenomicPosition"));
-const LegendBar_1 = __importDefault(require("../../shared/components/LegendBar"));
+const MultiVariantCrosshairs_1 = __importDefault(require("../../shared/components/MultiVariantCrosshairs"));
+const MultiVariantLegendBar_1 = __importDefault(require("../../shared/components/MultiVariantLegendBar"));
 const MultiLinearVariantMatrixDisplayComponent = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { lineZoneHeight } = model;
@@ -26,6 +26,6 @@ const MultiLinearVariantMatrixDisplayComponent = (0, mobx_react_1.observer)(func
         }, onMouseLeave: () => {
             setMouseY(undefined);
             setMouseX(undefined);
-        }, children: [(0, jsx_runtime_1.jsxs)("div", { style: { position: 'relative' }, children: [(0, jsx_runtime_1.jsx)(LinesConnectingMatrixToGenomicPosition_1.default, { model: model }), (0, jsx_runtime_1.jsxs)("div", { style: { position: 'absolute', top: lineZoneHeight }, children: [(0, jsx_runtime_1.jsx)(LegendBar_1.default, { model: model }), (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props })] })] }), mouseX && mouseY && mouseY > lineZoneHeight ? ((0, jsx_runtime_1.jsx)(Crosshair_1.default, { mouseX: mouseX, mouseY: mouseY, model: model })) : null] }));
+        }, children: [(0, jsx_runtime_1.jsxs)("div", { style: { position: 'relative' }, children: [(0, jsx_runtime_1.jsx)(LinesConnectingMatrixToGenomicPosition_1.default, { model: model }), (0, jsx_runtime_1.jsxs)("div", { style: { position: 'absolute', top: lineZoneHeight }, children: [(0, jsx_runtime_1.jsx)(MultiVariantLegendBar_1.default, { model: model }), (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props })] })] }), mouseX && mouseY && mouseY > lineZoneHeight ? ((0, jsx_runtime_1.jsx)(MultiVariantCrosshairs_1.default, { mouseX: mouseX, mouseY: mouseY, model: model })) : null] }));
 });
 exports.default = MultiLinearVariantMatrixDisplayComponent;

package/dist/MultiLinearVariantMatrixDisplay/index.js

@@ -13,7 +13,7 @@ function LinearVariantMatrixDisplayF(pluginManager) {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearVariantMatrixDisplay',
-            displayName: 'Multi-variant display (matrix)',
+            displayName: 'Multi-sample variant display (matrix)',
             configSchema,
             stateModel: (0, model_1.default)(configSchema),
             trackType: 'VariantTrack',

package/dist/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -89,6 +89,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    lengthCutoffFilter: import("mobx-state-tree").IType<number | undefined, number, number>;
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
+    referenceDrawingMode: import("mobx-state-tree").IType<string | undefined, string, string>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -236,19 +239,28 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
 } & {
     sourcesLoadingStopToken: string | undefined;
+    simplifiedFeaturesStopToken: string | undefined;
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
     sourcesVolatile: import("../shared/types").Source[] | undefined;
     featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
     hasPhased: boolean;
     sampleInfo: undefined | Record<string, import("../shared/types").SampleInfo>;
-    hoveredGenotype: string | undefined;
+    hoveredGenotype: {
+        genotype: string;
+        name: string;
+    } | undefined;
 } & {
+    setJexlFilters(f?: string[]): void;
     setRowHeight(arg: number): void;
-    setHoveredGenotype(arg: string): void;
+    setHoveredGenotype(arg?: {
+        genotype: string;
+        name: string;
+    }): void;
     setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
     setLayout(layout: import("../shared/types").Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
+    setSimplifiedFeaturesLoading(str: string): void;
     setSources(sources: import("../shared/types").Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
@@ -256,7 +268,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     setAutoHeight(arg: boolean): void;
     setHasPhased(arg: boolean): void;
     setSampleInfo(arg: Record<string, import("../shared/types").SampleInfo>): void;
+    setReferenceDrawingMode(arg: string): void;
 } & {
+    readonly activeFilters: any;
     readonly preSources: import("../shared/types").Source[] | undefined;
     readonly sourcesWithoutLayout: {
         label: string;
@@ -277,6 +291,17 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         HP?: number;
     }[] | undefined;
 } & {
+    readonly sourceMap: {
+        [k: string]: {
+            label: string;
+            id: string;
+            baseUri?: string;
+            name: string;
+            color?: string;
+            group?: string;
+            HP?: number;
+        };
+    } | undefined;
     readonly rowHeight: number;
     adapterProps(): any;
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
@@ -330,6 +355,18 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         type?: undefined;
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        type: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        icon?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {

package/dist/MultiLinearVariantMatrixDisplay/model.js

@@ -77,6 +77,7 @@ function stateModelFactory(configSchema) {
                 notReady: superProps.notReady || !self.sources || !self.featuresReady,
                 renderingMode: self.renderingMode,
                 minorAlleleFrequencyFilter: self.minorAlleleFrequencyFilter,
+                lengthCutoffFilter: self.lengthCutoffFilter,
                 height: self.totalHeight,
                 sources: self.sources,
             };

package/dist/MultiLinearVariantMatrixDisplay/renderSvg.js

@@ -8,10 +8,10 @@ const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
 const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./components/LinesConnectingMatrixToGenomicPosition"));
-const LegendBar_1 = __importDefault(require("../shared/components/LegendBar"));
+const MultiVariantLegendBar_1 = __importDefault(require("../shared/components/MultiVariantLegendBar"));
 async function renderSvg(model, opts, superRenderSvg) {
     await (0, mobx_1.when)(() => !!model.regionCannotBeRenderedText);
     const { offsetPx } = (0, util_1.getContainingView)(model);
     const { lineZoneHeight } = model;
-    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: [(0, jsx_runtime_1.jsx)(LinesConnectingMatrixToGenomicPosition_1.default, { exportSVG: true, model: model }), (0, jsx_runtime_1.jsxs)("g", { transform: `translate(0,${lineZoneHeight})`, children: [(0, jsx_runtime_1.jsx)("g", { children: await superRenderSvg(opts) }), (0, jsx_runtime_1.jsx)(LegendBar_1.default, { model: model, orientation: "left", exportSVG: true })] })] }) }));
+    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("g", { transform: `translate(${Math.max(-offsetPx, 0)})`, children: [(0, jsx_runtime_1.jsx)(LinesConnectingMatrixToGenomicPosition_1.default, { exportSVG: true, model: model }), (0, jsx_runtime_1.jsxs)("g", { transform: `translate(0,${lineZoneHeight})`, children: [(0, jsx_runtime_1.jsx)("g", { children: await superRenderSvg(opts) }), (0, jsx_runtime_1.jsx)(MultiVariantLegendBar_1.default, { model: model, orientation: "left", exportSVG: true })] })] }) }));
 }

package/dist/MultiLinearVariantMatrixRenderer/{LinearVariantMatrixRenderer.d.ts → MultiLinearVariantMatrixRenderer.d.ts}

@@ -1,30 +1,34 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { SimpleFeature } from '@jbrowse/core/util';
 import type { RenderArgsDeserialized } from './types';
 import type { Feature } from '@jbrowse/core/util';
 export default class LinearVariantMatrixRenderer extends BoxRendererType {
     supportsSVG: boolean;
     render(renderProps: RenderArgsDeserialized): Promise<{
         features: Map<any, any>;
-        simplifiedFeatures: any;
+        simplifiedFeatures: SimpleFeature[];
         height: number;
         width: number;
+        arr: string[][];
         canvasRecordedData: any;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
-        simplifiedFeatures: any;
+        simplifiedFeatures: SimpleFeature[];
         height: number;
         width: number;
+        arr: string[][];
         reactElement: import("react/jsx-runtime").JSX.Element;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
         html?: string;
     } | {
         features: Map<any, any>;
-        simplifiedFeatures: any;
+        simplifiedFeatures: SimpleFeature[];
         height: number;
         width: number;
+        arr: string[][];
         imageData: any;
         layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
         reactElement?: React.ReactElement;

package/dist/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.d.ts

@@ -0,0 +1,8 @@
+import type { MultiVariantBaseModel } from '../../shared/MultiVariantBaseModel';
+declare const MultiLinearVariantMatrixRendering: (props: {
+    width: number;
+    height: number;
+    displayModel: MultiVariantBaseModel;
+    arr: string[][];
+}) => import("react/jsx-runtime").JSX.Element;
+export default MultiLinearVariantMatrixRendering;

package/dist/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const MultiLinearVariantMatrixRendering = (0, mobx_react_1.observer)(function (props) {
+    const { arr, width, height, displayModel } = props;
+    const ref = (0, react_1.useRef)(null);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        var _a, _b, _c;
+        if (!ref.current) {
+            return;
+        }
+        const r = ref.current.getBoundingClientRect();
+        const offsetX = eventClientX - r.left;
+        const offsetY = eventClientY - r.top;
+        const dimY = arr.length;
+        const dimX = ((_a = arr[0]) === null || _a === void 0 ? void 0 : _a.length) || 0;
+        const name = (_b = displayModel.sources[Math.floor((offsetY / height) * dimX)]) === null || _b === void 0 ? void 0 : _b.name;
+        const genotype = (_c = arr[Math.floor((offsetX / width) * dimY)]) === null || _c === void 0 ? void 0 : _c[Math.floor((offsetY / height) * dimX)];
+        return genotype && name
+            ? {
+                name,
+                genotype,
+            }
+            : undefined;
+    }
+    return ((0, jsx_runtime_1.jsx)("div", { ref: ref, onMouseMove: e => {
+            displayModel.setHoveredGenotype(getFeatureUnderMouse(e.clientX, e.clientY));
+        }, onMouseLeave: () => {
+            displayModel.setHoveredGenotype(undefined);
+        }, onMouseOut: () => {
+            displayModel.setHoveredGenotype(undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height,
+        }, children: (0, jsx_runtime_1.jsx)(ui_1.PrerenderedCanvas, { ...props }) }));
+});
+exports.default = MultiLinearVariantMatrixRendering;

package/dist/MultiLinearVariantMatrixRenderer/index.js

@@ -4,15 +4,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LinearVariantMatrixRendererF;
-const LinearVariantMatrixRenderer_1 = __importDefault(require("./LinearVariantMatrixRenderer"));
-const LinearVariantMatrixRendering_1 = __importDefault(require("./components/LinearVariantMatrixRendering"));
+const MultiLinearVariantMatrixRenderer_1 = __importDefault(require("./MultiLinearVariantMatrixRenderer"));
+const MultiLinearVariantMatrixRendering_1 = __importDefault(require("./components/MultiLinearVariantMatrixRendering"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function LinearVariantMatrixRendererF(pluginManager) {
     pluginManager.addRendererType(() => {
-        return new LinearVariantMatrixRenderer_1.default({
+        return new MultiLinearVariantMatrixRenderer_1.default({
             name: 'LinearVariantMatrixRenderer',
             displayName: 'Linear variant matrix renderer',
-            ReactComponent: LinearVariantMatrixRendering_1.default,
+            ReactComponent: MultiLinearVariantMatrixRendering_1.default,
             configSchema: configSchema_1.default,
             pluginManager,
         });

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.d.ts

@@ -1,9 +1,9 @@
-import type { RenderArgsDeserializedWithFeaturesAndLayout } from './types';
+import type { RenderArgsDeserialized } from './types';
 export declare function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }: {
     ctx: CanvasRenderingContext2D;
     canvasWidth: number;
     canvasHeight: number;
-    renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+    renderArgs: RenderArgsDeserialized;
 }): Promise<{
     mafs: {
         feature: import("@jbrowse/core/util").Feature;

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -8,29 +8,28 @@ const drawAlleleCount_1 = require("../shared/drawAlleleCount");
 const drawPhased_1 = require("../shared/drawPhased");
 const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
 async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
-    const { renderingMode: renderingMode, minorAlleleFrequencyFilter, sources, features, stopToken, } = renderArgs;
+    const { renderingMode, minorAlleleFrequencyFilter, sources, features, stopToken, lengthCutoffFilter, } = renderArgs;
     const { statusCallback = () => { } } = renderArgs;
     const h = canvasHeight / sources.length;
     (0, stopToken_1.checkStopToken)(stopToken);
-    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(features.values(), minorAlleleFrequencyFilter);
+    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
+        stopToken,
+        features: features.values(),
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+    });
     (0, stopToken_1.checkStopToken)(stopToken);
     const arr = [];
     const m = mafs.length;
     const w = canvasWidth / m;
     await (0, util_1.updateStatus)('Drawing variant matrix', statusCallback, () => {
-        var _a, _b, _c;
-        let start = performance.now();
-        for (let i = 0; i < m; i++) {
-            if (performance.now() - start > 400) {
-                (0, stopToken_1.checkStopToken)(stopToken);
-                start = performance.now();
-            }
+        (0, util_1.forEachWithStopTokenCheck)(mafs, stopToken, ({ feature, mostFrequentAlt }, idx) => {
+            var _a, _b, _c;
             const arr2 = [];
-            const { feature, mostFrequentAlt } = mafs[i];
             const hasPhaseSet = (_a = feature.get('FORMAT')) === null || _a === void 0 ? void 0 : _a.includes('PS');
             if (hasPhaseSet) {
                 const samp = feature.get('samples');
-                const x = (i / mafs.length) * canvasWidth;
+                const x = (idx / mafs.length) * canvasWidth;
                 const sln = sources.length;
                 for (let j = 0; j < sln; j++) {
                     const y = (j / sln) * canvasHeight;
@@ -62,7 +61,7 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
             }
             else {
                 const samp = feature.get('genotypes');
-                const x = (i / mafs.length) * canvasWidth;
+                const x = (idx / mafs.length) * canvasWidth;
                 const sln = sources.length;
                 for (let j = 0; j < sln; j++) {
                     const y = (j / sln) * canvasHeight;
@@ -89,7 +88,7 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                 }
             }
             arr.push(arr2);
-        }
+        });
     });
     return {
         mafs,

package/dist/MultiLinearVariantMatrixRenderer/types.d.ts

@@ -6,11 +6,9 @@ export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
     minorAlleleFrequencyFilter: number;
     highResolutionScaling: number;
     height: number;
-    renderingMode: string;
-}
-export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
-    sources: Source[];
     features: Map<string, Feature>;
     renderingMode: string;
     statusCallback?: (arg: string) => void;
+    lengthCutoffFilter: number;
+    stopToken: string;
 }

package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts

@@ -8,6 +8,16 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
+        rbush: any;
+        featureGenotypeMap: {
+            [k: string]: {
+                alt: any;
+                ref: any;
+                name: any;
+                description: any;
+                length: number;
+            };
+        };
         canvasRecordedData: any;
         reactElement?: React.ReactElement;
         html?: string;
@@ -16,6 +26,16 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
+        rbush: any;
+        featureGenotypeMap: {
+            [k: string]: {
+                alt: any;
+                ref: any;
+                name: any;
+                description: any;
+                length: number;
+            };
+        };
         reactElement: import("react/jsx-runtime").JSX.Element;
         html?: string;
     } | {
@@ -23,9 +43,18 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
+        rbush: any;
+        featureGenotypeMap: {
+            [k: string]: {
+                alt: any;
+                ref: any;
+                name: any;
+                description: any;
+                length: number;
+            };
+        };
         imageData: any;
         reactElement?: React.ReactElement;
         html?: string;
     }>;
 }
-export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.js

@@ -45,14 +45,20 @@ class MultiVariantBaseRenderer extends FeatureRendererType_1.default {
     }
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
-        const { height, regions, bpPerPx } = renderProps;
+        const { height, referenceDrawingMode, regions, bpPerPx } = renderProps;
         const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
         const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
-        const rest = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => makeImageData(ctx, {
-            ...renderProps,
-            features,
-        }));
+        const rest = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => {
+            if (referenceDrawingMode === 'skip') {
+                ctx.fillStyle = '#ccc';
+                ctx.fillRect(0, 0, width, height);
+            }
+            return makeImageData(ctx, {
+                ...renderProps,
+                features,
+            });
+        });
         const results = await super.render({
             ...renderProps,
             ...rest,

package/dist/MultiLinearVariantRenderer/components/{MultiVariantRendering.d.ts → MultiLinearVariantRendering.d.ts}

@@ -1,7 +1,14 @@
-import RBush from 'rbush';
 import type { Source } from '../../shared/types';
 import type { Feature } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
+type SerializedRBush = any;
+interface MinimizedVariantRecord {
+    alt: string[];
+    ref: string;
+    name: string;
+    description: string;
+    length: number;
+}
 declare const MultiVariantRendering: (props: {
     regions: Region[];
     features: Map<string, Feature>;
@@ -10,10 +17,9 @@ declare const MultiVariantRendering: (props: {
     height: number;
     sources: Source[];
     scrollTop: number;
+    featureGenotypeMap: Record<string, MinimizedVariantRecord>;
     totalHeight: number;
-    rbush: RBush<{
-        genotype: string;
-    }>;
+    rbush: SerializedRBush;
     displayModel: any;
     onMouseLeave?: (event: React.MouseEvent) => void;
     onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void;