@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/MultiLinearVariantDisplay/renderSvg.d.ts

@@ -1,3 +0,0 @@
-import type { MultiLinearVariantDisplayModel } from './model';
-import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
-export declare function renderSvg(self: MultiLinearVariantDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<import("react/jsx-runtime").JSX.Element>;

package/dist/MultiLinearVariantDisplay/renderSvg.js

@@ -1,15 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSvg = renderSvg;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const mobx_1 = require("mobx");
-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)(MultiVariantLegendBar_1.default, { model: self, orientation: "left", exportSVG: true }) })] }));
-}

package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts

@@ -1,6 +0,0 @@
-import type { MultiLinearVariantMatrixDisplayModel } from '../model';
-declare const LinesConnectingMatrixToGenomicPosition: ({ model, exportSVG, }: {
-    model: MultiLinearVariantMatrixDisplayModel;
-    exportSVG?: boolean;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default LinesConnectingMatrixToGenomicPosition;

package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js

@@ -1,83 +0,0 @@
-"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");
-const useStyles = (0, mui_1.makeStyles)()({
-    resizeHandle: {
-        height: 4,
-        background: '#ccc',
-        boxSizing: 'border-box',
-        borderTop: '1px solid #fafafa',
-    },
-});
-const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSVG, }) {
-    const { height } = model;
-    const { width, offsetPx } = (0, util_1.getContainingView)(model);
-    const left = Math.max(0, -offsetPx);
-    return exportSVG ? ((0, jsx_runtime_1.jsx)("g", { transform: `translate(${left})`, children: children })) : ((0, jsx_runtime_1.jsx)("svg", { style: {
-            position: 'absolute',
-            top: 0,
-            left,
-            height,
-            width,
-        }, children: children }));
-});
-const LinesConnectingMatrixToGenomicPosition = (0, mobx_react_1.observer)(function ({ model, exportSVG, }) {
-    var _a;
-    const { classes } = useStyles();
-    const { assemblyManager } = (0, util_1.getSession)(model);
-    const view = (0, util_1.getContainingView)(model);
-    const [mouseOverLine, setMouseOverLine] = (0, react_1.useState)();
-    const { lineZoneHeight, featuresVolatile } = model;
-    const { assemblyNames, dynamicBlocks } = view;
-    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.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);
-    const view = (0, util_1.getContainingView)(model);
-    const { lineZoneHeight, featuresVolatile } = model;
-    const { offsetPx, assemblyNames, dynamicBlocks } = view;
-    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);
-    const l = Math.max(offsetPx, 0);
-    return assembly && featuresVolatile ? ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: featuresVolatile.map((f, i) => {
-            var _a;
-            const ref = f.get('refName');
-            const c = (((_a = view.bpToPx({
-                refName: assembly.getCanonicalRefName(ref) || ref,
-                coord: f.get('start'),
-            })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - l;
-            return ((0, jsx_runtime_1.jsx)("line", { stroke: "#0004", strokeWidth: 1, x1: i * w + w / 2, x2: c, y1: lineZoneHeight, y2: 0, onMouseEnter: () => {
-                    setMouseOverLine({ f, idx: i, c });
-                }, onMouseLeave: () => {
-                    setMouseOverLine(undefined);
-                } }, f.id()));
-        }) })) : null;
-});
-exports.default = LinesConnectingMatrixToGenomicPosition;

package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.d.ts

@@ -1,5 +0,0 @@
-import type { MultiLinearVariantMatrixDisplayModel } from '../model';
-declare const MultiLinearVariantMatrixDisplayComponent: (props: {
-    model: MultiLinearVariantMatrixDisplayModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default MultiLinearVariantMatrixDisplayComponent;

package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js

@@ -1,31 +0,0 @@
-"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 plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_react_1 = require("mobx-react");
-const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./LinesConnectingMatrixToGenomicPosition"));
-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;
-    const ref = (0, react_1.useRef)(null);
-    const [mouseY, setMouseY] = (0, react_1.useState)();
-    const [mouseX, setMouseX] = (0, react_1.useState)();
-    return ((0, jsx_runtime_1.jsxs)("div", { ref: ref, onMouseMove: event => {
-            var _a;
-            const rect = (_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect();
-            const top = (rect === null || rect === void 0 ? void 0 : rect.top) || 0;
-            const left = (rect === null || rect === void 0 ? void 0 : rect.left) || 0;
-            setMouseY(event.clientY - top);
-            setMouseX(event.clientX - left);
-        }, 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)(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/configSchema.d.ts

@@ -1,37 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    height: {
-        type: string;
-        defaultValue: number;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("mobx-state-tree").IAnyModelType;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/dist/MultiLinearVariantMatrixDisplay/configSchema.js

@@ -1,22 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = configSchemaF;
-const configuration_1 = require("@jbrowse/core/configuration");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const configSchema_1 = __importDefault(require("../MultiLinearVariantMatrixRenderer/configSchema"));
-function x() { }
-function configSchemaF(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('LinearVariantMatrixDisplay', {
-        renderer: configSchema_1.default,
-        height: {
-            type: 'number',
-            defaultValue: 250,
-        },
-    }, {
-        baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
-        explicitlyTyped: true,
-    });
-}

package/dist/MultiLinearVariantMatrixDisplay/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function LinearVariantMatrixDisplayF(pluginManager: PluginManager): void;

package/dist/MultiLinearVariantMatrixDisplay/index.js

@@ -1,24 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LinearVariantMatrixDisplayF;
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const VariantDisplayComponent_1 = __importDefault(require("./components/VariantDisplayComponent"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function LinearVariantMatrixDisplayF(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.default)(pluginManager);
-        return new DisplayType_1.default({
-            name: 'LinearVariantMatrixDisplay',
-            displayName: 'Multi-sample variant display (matrix)',
-            configSchema,
-            stateModel: (0, model_1.default)(configSchema),
-            trackType: 'VariantTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: VariantDisplayComponent_1.default,
-        });
-    });
-}