@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/esm/LinearVariantDisplay/model.d.ts

@@ -1,13 +1,6 @@
-import { Feature } from '@jbrowse/core/util';
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-/**
- * #stateModel LinearVariantDisplay
- * similar to basic display, but provides custom widget on feature click
- * extends
- *
- * - [LinearBasicDisplay](../linearbasicdisplay)
- */
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
+import type { Instance } from 'mobx-state-tree';
 export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -20,21 +13,12 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
@@ -52,21 +36,15 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -108,13 +86,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     configuration: AnyConfigurationSchemaType;
     jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LinearVariantDisplay">;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
@@ -205,14 +177,15 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -239,7 +212,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     readonly activeFilters: any;
@@ -283,9 +256,6 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     };
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {
-    /**
-     * #action
-     */
     selectFeature(feature: Feature): Promise<void>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type LinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;

package/esm/LinearVariantDisplay/model.js

@@ -1,31 +1,15 @@
-import { getConf, ConfigurationReference } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
+import { getContainingTrack, getContainingView, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { getContainingTrack, getSession, getContainingView, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
-/**
- * #stateModel LinearVariantDisplay
- * similar to basic display, but provides custom widget on feature click
- * extends
- *
- * - [LinearBasicDisplay](../linearbasicdisplay)
- */
 export default function stateModelFactory(configSchema) {
     return types
         .compose('LinearVariantDisplay', linearBasicDisplayModelFactory(configSchema), types.model({
-        /**
-         * #property
-         */
         type: types.literal('LinearVariantDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         async selectFeature(feature) {
             const session = getSession(self);
             if (isSessionModelWithWidgets(session)) {

package/esm/MultiLinearVariantDisplay/components/Crosshair.d.ts

@@ -0,0 +1,7 @@
+import type { MultiLinearVariantDisplayModel } from '../model';
+declare const Crosshair: ({ mouseX, mouseY, model, }: {
+    mouseX: number;
+    mouseY: number;
+    model: MultiLinearVariantDisplayModel;
+}) => import("react/jsx-runtime").JSX.Element | null;
+export default Crosshair;

package/esm/MultiLinearVariantDisplay/components/Crosshair.js

@@ -0,0 +1,30 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { getContainingView } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import MultiVariantTooltip from '../../shared/MultiVariantTooltip';
+const useStyles = makeStyles()({
+    rel: {
+        position: 'relative',
+    },
+    cursor: {
+        pointerEvents: 'none',
+        zIndex: 1000,
+        position: 'absolute',
+    },
+    color: {
+        width: 10,
+        height: 10,
+    },
+});
+const Crosshair = observer(function ({ mouseX, mouseY, model, }) {
+    const { classes } = useStyles();
+    const { hoveredGenotype, height, scrollTop, rowHeight, sources } = model;
+    const { width } = getContainingView(model);
+    const source = sources === null || sources === void 0 ? void 0 : sources[Math.floor(mouseY / rowHeight)];
+    const y = mouseY - scrollTop;
+    return source ? (_jsxs("div", { className: classes.rel, children: [_jsxs("svg", { className: classes.cursor, width: width, height: height, style: {
+                    top: scrollTop,
+                }, children: [_jsx("line", { x1: 0, x2: width, y1: y, y2: y, stroke: "black" }), _jsx("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })] }), _jsx(MultiVariantTooltip, { source: { ...source, hoveredGenotype } })] })) : null;
+});
+export default Crosshair;

package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.d.ts

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

package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.js

@@ -0,0 +1,24 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useRef, useState } from 'react';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
+import { observer } from 'mobx-react';
+import Crosshair from './Crosshair';
+import LegendBar from '../../shared/LegendBar';
+const MultiLinearVariantDisplayComponent = observer(function (props) {
+    const { model } = props;
+    const ref = useRef(null);
+    const [mouseY, setMouseY] = useState();
+    const [mouseX, setMouseX] = useState();
+    return (_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: [_jsx(BaseLinearDisplayComponent, { ...props }), _jsx(LegendBar, { model: model }), mouseX && mouseY ? (_jsx(Crosshair, { mouseX: mouseX, mouseY: mouseY, model: model })) : null] }));
+});
+export default MultiLinearVariantDisplayComponent;

package/esm/MultiLinearVariantDisplay/configSchema.d.ts

@@ -0,0 +1,80 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function VariantConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    defaultRendering: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+    };
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        MultiVariantRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, 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<{
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    minimalTicks: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    numStdDev: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+}, 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/esm/MultiLinearVariantDisplay/configSchema.js

@@ -0,0 +1,24 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+import sharedVariantConfigFactory from '../shared/SharedVariantConfigSchema';
+function x() { }
+export default function VariantConfigFactory(pluginManager) {
+    const MultiVariantRendererConfigSchema = pluginManager.getRendererType('MultiVariantRenderer').configSchema;
+    return ConfigurationSchema('MultiLinearVariantDisplay', {
+        defaultRendering: {
+            type: 'stringEnum',
+            model: types.enumeration('Rendering', ['multivariant']),
+            defaultValue: 'multivariant',
+        },
+        renderers: ConfigurationSchema('RenderersConfiguration', {
+            MultiVariantRenderer: MultiVariantRendererConfigSchema,
+        }),
+        height: {
+            type: 'number',
+            defaultValue: 200,
+        },
+    }, {
+        baseConfiguration: sharedVariantConfigFactory(),
+        explicitlyTyped: true,
+    });
+}

package/esm/MultiLinearVariantDisplay/index.d.ts

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

package/esm/MultiLinearVariantDisplay/index.js

@@ -0,0 +1,18 @@
+import { lazy } from 'react';
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import configSchemaFactory from './configSchema';
+import modelFactory from './model';
+export default function MultiLinearVariantDisplayF(pluginManager) {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        return new DisplayType({
+            name: 'MultiLinearVariantDisplay',
+            displayName: 'Multi-variant display (regular)',
+            configSchema,
+            stateModel: modelFactory(configSchema),
+            trackType: 'VariantTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: lazy(() => import('./components/VariantDisplayComponent')),
+        });
+    });
+}