@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/esm/LinearVariantDisplay/model.js

@@ -1,34 +1,18 @@
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
-import { getContainingTrack, getContainingView, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view';
-import { types } from 'mobx-state-tree';
+import { ConfigurationReference } from '@jbrowse/core/configuration';
+import { types } from '@jbrowse/mobx-state-tree';
+import { linearFeatureDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view';
 export default function stateModelFactory(configSchema) {
     return types
-        .compose('LinearVariantDisplay', linearBasicDisplayModelFactory(configSchema), types.model({
+        .compose('LinearVariantDisplay', linearFeatureDisplayModelFactory(configSchema), types.model({
         type: types.literal('LinearVariantDisplay'),
         configuration: ConfigurationReference(configSchema),
     }))
-        .actions(self => ({
-        async selectFeature(feature) {
-            const session = getSession(self);
-            if (isSessionModelWithWidgets(session)) {
-                const { rpcManager } = session;
-                const sessionId = getRpcSessionId(self);
-                const track = getContainingTrack(self);
-                const view = getContainingView(self);
-                const adapterConfig = getConf(track, 'adapter');
-                const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
-                    adapterConfig,
-                });
-                session.showWidget(session.addWidget('VariantFeatureWidget', 'variantFeature', {
-                    featureData: feature.toJSON(),
-                    view,
-                    track,
-                    descriptions,
-                }));
-            }
-            session.setSelection(feature);
+        .views(() => ({
+        get featureWidgetType() {
+            return {
+                type: 'VariantFeatureWidget',
+                id: 'variantFeature',
+            };
         },
     }));
 }

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

@@ -1,4 +1,4 @@
-import type { MultiLinearVariantDisplayModel } from '../model';
+import type { MultiLinearVariantDisplayModel } from '../model.ts';
 declare const MultiLinearVariantDisplayComponent: (props: {
     model: MultiLinearVariantDisplayModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.js

@@ -1,24 +1,14 @@
 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 { useRef } from 'react';
 import { observer } from 'mobx-react';
-import Crosshair from '../../shared/components/MultiVariantCrosshairs';
-import LegendBar from '../../shared/components/MultiVariantLegendBar';
-const MultiLinearVariantDisplayComponent = observer(function (props) {
+import Crosshair from "../../shared/components/MultiVariantCrosshairs.js";
+import ScrollableVariantContainer from "../../shared/components/ScrollableVariantContainer.js";
+import { useMouseTracking } from "../../shared/hooks/useMouseTracking.js";
+const MultiLinearVariantDisplayComponent = observer(function MultiLinearVariantDisplayComponent(props) {
     const { model } = props;
+    const { height } = model;
     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] }));
+    const { mouseState, handleMouseMove, handleMouseLeave } = useMouseTracking(ref);
+    return (_jsxs("div", { ref: ref, style: { position: 'relative', height }, onMouseMove: handleMouseMove, onMouseLeave: handleMouseLeave, children: [_jsx(ScrollableVariantContainer, { model: model }), mouseState ? (_jsx(Crosshair, { mouseX: mouseState.x, mouseY: mouseState.y, offsetX: mouseState.offsetX, offsetY: mouseState.offsetY, model: model })) : null] }));
 });
 export default MultiLinearVariantDisplayComponent;

package/esm/MultiLinearVariantDisplay/configSchema.d.ts

@@ -1,56 +1,18 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function VariantConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function VariantConfigFactory(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
     defaultRendering: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
+        model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         defaultValue: string;
     };
-    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderers: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         MultiVariantRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").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<{
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
         description: string;
@@ -77,4 +39,4 @@ export default function VariantConfigFactory(pluginManager: PluginManager): impo
         description: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;

package/esm/MultiLinearVariantDisplay/configSchema.js

@@ -1,6 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-import sharedVariantConfigFactory from '../shared/SharedVariantConfigSchema';
+import { types } from '@jbrowse/mobx-state-tree';
+import sharedVariantConfigFactory from "../shared/SharedVariantConfigSchema.js";
 function x() { }
 export default function VariantConfigFactory(pluginManager) {
     const MultiVariantRendererConfigSchema = pluginManager.getRendererType('MultiVariantRenderer').configSchema;

package/esm/MultiLinearVariantDisplay/index.js

@@ -1,18 +1,19 @@
 import { lazy } from 'react';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-import configSchemaFactory from './configSchema';
-import modelFactory from './model';
+import configSchemaFactory from "./configSchema.js";
+import modelFactory from "./model.js";
 export default function MultiLinearVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
             name: 'MultiLinearVariantDisplay',
             displayName: 'Multi-sample variant display (regular)',
+            helpText: 'Draws multi-sample variant data using a row for each sample in your dataset. The term "regular" is unfortunately vague but it just means drawing the variants at their actual base pair coordinates. The "regular" mode is notable for also being able to draw structural variants (SVs), including overlapping SVs. It will specifically skip drawing the "reference" alleles by default, allowing overlapping SVs to not cover each other up',
             configSchema,
             stateModel: modelFactory(configSchema),
             trackType: 'VariantTrack',
             viewType: 'LinearGenomeView',
-            ReactComponent: lazy(() => import('./components/VariantDisplayComponent')),
+            ReactComponent: lazy(() => import("./components/VariantDisplayComponent.js")),
         });
     });
 }