@jbrowse/plugin-wiggle 3.6.5 → 4.0.0

package/esm/getQuantitativeStats.js

@@ -1,19 +1,22 @@
 import { getConf } from '@jbrowse/core/configuration';
-import { getContainingView, getSession } from '@jbrowse/core/util';
+import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { isAlive } from 'mobx-state-tree';
+import { isAlive } from '@jbrowse/mobx-state-tree';
 export async function getQuantitativeStats(self, opts) {
     const { rpcManager } = getSession(self);
     const numStdDev = getConf(self, 'numStdDev') || 3;
-    const { adapterConfig, autoscaleType } = self;
+    const { adapterConfig, autoscaleType, effectiveRpcDriverName } = self;
     const sessionId = getRpcSessionId(self);
+    const trackInstanceId = getContainingTrack(self).id;
     const { currStatsBpPerPx } = opts;
     const params = {
         sessionId,
+        trackInstanceId,
         adapterConfig,
+        rpcDriverName: effectiveRpcDriverName,
         statusCallback: (message) => {
             if (isAlive(self)) {
-                self.setMessage(message);
+                self.setStatusMessage(message);
             }
         },
         ...opts,
@@ -33,8 +36,8 @@ export async function getQuantitativeStats(self, opts) {
                 currStatsBpPerPx,
             };
     }
-    if (autoscaleType === 'local' || autoscaleType === 'localsd') {
-        const { dynamicBlocks, bpPerPx } = getContainingView(self);
+    else if (autoscaleType === 'local' || autoscaleType === 'localsd') {
+        const { dynamicBlocks, staticBlocks, bpPerPx } = getContainingView(self);
         const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionQuantitativeStats', {
             ...params,
             regions: dynamicBlocks.contentBlocks.map(region => {
@@ -45,6 +48,14 @@ export async function getQuantitativeStats(self, opts) {
                     end: Math.ceil(end),
                 };
             }),
+            staticBlocks: staticBlocks.contentBlocks.map(region => {
+                const { start, end } = region;
+                return {
+                    ...JSON.parse(JSON.stringify(region)),
+                    start: Math.floor(start),
+                    end: Math.ceil(end),
+                };
+            }),
             bpPerPx,
         }));
         const { scoreMin, scoreMean, scoreStdDev } = results;
@@ -60,7 +71,7 @@ export async function getQuantitativeStats(self, opts) {
                 currStatsBpPerPx,
             };
     }
-    if (autoscaleType === 'zscale') {
+    else if (autoscaleType === 'zscale') {
         return rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params);
     }
     throw new Error(`invalid autoscaleType '${autoscaleType}'`);

package/esm/getQuantitativeStatsAutorun.d.ts

@@ -1,13 +1,14 @@
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { QuantitativeStats } from '@jbrowse/core/util/stats';
+import type { StopToken } from '@jbrowse/core/util/stopToken';
 export declare function getQuantitativeStatsAutorun(self: {
     quantitativeStatsReady: boolean;
     configuration: AnyConfigurationModel;
     adapterConfig: AnyConfigurationModel;
     autoscaleType: string;
     adapterProps: () => Record<string, unknown>;
-    setStatsLoading: (token: string) => void;
+    setStatsLoading: (token: StopToken) => void;
     setError: (error: unknown) => void;
-    setMessage: (str: string) => void;
+    setStatusMessage: (str: string) => void;
     updateQuantitativeStats: (stats: QuantitativeStats, region: string) => void;
 }): void;

package/esm/getQuantitativeStatsAutorun.js

@@ -1,8 +1,8 @@
 import { getContainingView, isAbortException } from '@jbrowse/core/util';
 import { createStopToken } from '@jbrowse/core/util/stopToken';
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { addDisposer, isAlive } from 'mobx-state-tree';
-import { getQuantitativeStats } from './getQuantitativeStats';
+import { getQuantitativeStats } from "./getQuantitativeStats.js";
 export function getQuantitativeStatsAutorun(self) {
     addDisposer(self, autorun(async () => {
         try {
@@ -28,5 +28,5 @@ export function getQuantitativeStatsAutorun(self) {
                 self.setError(e);
             }
         }
-    }, { delay: 1000 }));
+    }, { delay: 500 }));
 }

package/esm/index.d.ts

@@ -1,15 +1,14 @@
 import Plugin from '@jbrowse/core/Plugin';
-import { modelFactory as linearWiggleDisplayModelFactory } from './LinearWiggleDisplay';
-import WiggleBaseRenderer from './WiggleBaseRenderer';
-import { XYPlotRenderer } from './XYPlotRenderer';
-import * as utils from './util';
+import { modelFactory as linearWiggleDisplayModelFactory } from './LinearWiggleDisplay/index.ts';
+import { XYPlotRenderer } from './XYPlotRenderer/index.ts';
+import * as utils from './util.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 export default class WigglePlugin extends Plugin {
     name: string;
     install(pm: PluginManager): void;
     exports: {
         LinearWiggleDisplayReactComponent: (props: {
-            model: import("./LinearWiggleDisplay/model").WiggleDisplayModel;
+            model: import("./LinearWiggleDisplay/model.ts").WiggleDisplayModel;
         }) => import("react/jsx-runtime").JSX.Element;
         XYPlotRendererReactComponent: (props: {
             regions: import("@jbrowse/core/util").Region[];
@@ -18,14 +17,11 @@ export default class WigglePlugin extends Plugin {
             width: number;
             height: number;
             blockKey: string;
-            onMouseLeave?: (event: React.MouseEvent) => void;
-            onMouseMove?: (event: React.MouseEvent, arg?: string) => void;
-            onFeatureClick?: (event: React.MouseEvent, arg?: string) => void;
+            displayModel: import("@jbrowse/plugin-linear-genome-view").BaseLinearDisplayModel;
         }) => import("react/jsx-runtime").JSX.Element;
         XYPlotRenderer: typeof XYPlotRenderer;
-        WiggleBaseRenderer: typeof WiggleBaseRenderer;
         linearWiggleDisplayModelFactory: typeof linearWiggleDisplayModelFactory;
-        xyPlotRendererConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        xyPlotRendererConfigSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
             filled: {
                 type: string;
                 defaultValue: boolean;
@@ -37,7 +33,7 @@ export default class WigglePlugin extends Plugin {
             };
             summaryScoreMode: {
                 type: string;
-                model: import("mobx-state-tree").ISimpleType<string>;
+                model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
                 description: string;
                 defaultValue: string;
             };
@@ -45,7 +41,7 @@ export default class WigglePlugin extends Plugin {
                 type: string;
                 defaultValue: number;
             };
-        }, 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<{
             color: {
                 type: string;
                 description: string;
@@ -71,7 +67,7 @@ export default class WigglePlugin extends Plugin {
             };
             bicolorPivot: {
                 type: string;
-                model: import("mobx-state-tree").ISimpleType<string>;
+                model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
                 description: string;
                 defaultValue: string;
             };
@@ -80,12 +76,12 @@ export default class WigglePlugin extends Plugin {
                 defaultValue: number;
                 description: string;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
+        }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
         utils: typeof utils;
     };
 }
-export * from './util';
-export { default as WiggleRendering } from './WiggleRendering';
-export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
-export type { TooltipContentsComponent } from './Tooltip';
-export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';
+export * from './util.ts';
+export { default as WiggleRendering } from './WiggleRendering.tsx';
+export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay/index.ts';
+export type { TooltipContentsComponent } from './Tooltip.tsx';
+export type { MultiRenderArgsDeserialized, RenderArgsDeserialized, RenderArgsDeserializedWithFeatures, } from './types.ts';

package/esm/index.js

@@ -1,38 +1,25 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BigWigAdapterF from './BigWigAdapter';
-import CreateMultiWiggleExtensionF from './CreateMultiWiggleExtension';
-import DensityRendererF from './DensityRenderer';
-import GuessAdapterF from './GuessAdapter';
-import LinePlotRendererF from './LinePlotRenderer';
-import LinearWiggleDisplayF, { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
-import MultiDensityRendererF from './MultiDensityRenderer';
-import MultiLineRendererF from './MultiLineRenderer';
-import MultiLinearWiggleDisplayF from './MultiLinearWiggleDisplay';
-import MultiQuantitativeTrackF from './MultiQuantitativeTrack';
-import MultiRowLineRendererF from './MultiRowLineRenderer';
-import MultiRowXYPlotRendererF from './MultiRowXYPlotRenderer';
-import MultiWiggleAdapterF from './MultiWiggleAdapter';
-import MultiWiggleAddTrackWorkflowF from './MultiWiggleAddTrackWorkflow';
-import MultiXYPlotRendererF from './MultiXYPlotRenderer';
-import QuantitativeTrackF from './QuantitativeTrack';
-import WiggleBaseRenderer from './WiggleBaseRenderer';
-import { MultiWiggleClusterScoreMatrix, MultiWiggleGetScoreMatrix, MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from './WiggleRPC/rpcMethods';
-import XYPlotRendererF, { ReactComponent as XYPlotRendererReactComponent, XYPlotRenderer, configSchema as xyPlotRendererConfigSchema, } from './XYPlotRenderer';
-import * as utils from './util';
+import BigWigAdapterF from "./BigWigAdapter/index.js";
+import CreateMultiWiggleExtensionF from "./CreateMultiWiggleExtension/index.js";
+import DensityRendererF from "./DensityRenderer/index.js";
+import GuessAdapterF from "./GuessAdapter/index.js";
+import LinePlotRendererF from "./LinePlotRenderer/index.js";
+import LinearWiggleDisplayF, { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from "./LinearWiggleDisplay/index.js";
+import MultiDensityRendererF from "./MultiDensityRenderer/index.js";
+import MultiLineRendererF from "./MultiLineRenderer/index.js";
+import MultiLinearWiggleDisplayF from "./MultiLinearWiggleDisplay/index.js";
+import MultiQuantitativeTrackF from "./MultiQuantitativeTrack/index.js";
+import MultiRowLineRendererF from "./MultiRowLineRenderer/index.js";
+import MultiRowXYPlotRendererF from "./MultiRowXYPlotRenderer/index.js";
+import MultiWiggleAdapterF from "./MultiWiggleAdapter/index.js";
+import MultiWiggleAddTrackWorkflowF from "./MultiWiggleAddTrackWorkflow/index.js";
+import MultiXYPlotRendererF from "./MultiXYPlotRenderer/index.js";
+import QuantitativeTrackF from "./QuantitativeTrack/index.js";
+import { MultiWiggleClusterScoreMatrix, MultiWiggleGetScoreMatrix, MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from "./WiggleRPC/rpcMethods.js";
+import XYPlotRendererF, { ReactComponent as XYPlotRendererReactComponent, XYPlotRenderer, configSchema as xyPlotRendererConfigSchema, } from "./XYPlotRenderer/index.js";
+import * as utils from "./util.js";
 export default class WigglePlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'WigglePlugin';
-        this.exports = {
-            LinearWiggleDisplayReactComponent,
-            XYPlotRendererReactComponent,
-            XYPlotRenderer,
-            WiggleBaseRenderer,
-            linearWiggleDisplayModelFactory,
-            xyPlotRendererConfigSchema,
-            utils,
-        };
-    }
+    name = 'WigglePlugin';
     install(pm) {
         MultiWiggleAdapterF(pm);
         BigWigAdapterF(pm);
@@ -57,8 +44,15 @@ export default class WigglePlugin extends Plugin {
         pm.addRpcMethod(() => new MultiWiggleGetScoreMatrix(pm));
         pm.addRpcMethod(() => new MultiWiggleClusterScoreMatrix(pm));
     }
+    exports = {
+        LinearWiggleDisplayReactComponent,
+        XYPlotRendererReactComponent,
+        XYPlotRenderer,
+        linearWiggleDisplayModelFactory,
+        xyPlotRendererConfigSchema,
+        utils,
+    };
 }
-export * from './util';
-export { default as WiggleRendering } from './WiggleRendering';
-export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
-export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';
+export * from "./util.js";
+export { default as WiggleRendering } from "./WiggleRendering.js";
+export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from "./LinearWiggleDisplay/index.js";

package/esm/multiRendererHelper.d.ts

@@ -0,0 +1,7 @@
+import type { MultiRenderArgsDeserialized } from './types.ts';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { RenderReturn } from '@jbrowse/core/pluggableElementTypes/renderers/RendererType';
+import type { Feature } from '@jbrowse/core/util';
+type RenderFeaturesFn = (props: MultiRenderArgsDeserialized, features: Feature[]) => Promise<RenderReturn>;
+export declare function renderMultiWiggle(pluginManager: PluginManager, renderProps: MultiRenderArgsDeserialized, renderFeatures: RenderFeaturesFn): Promise<RenderReturn>;
+export {};

package/esm/multiRendererHelper.js

@@ -0,0 +1,12 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
+export async function renderMultiWiggle(pluginManager, renderProps, renderFeatures) {
+    const { sessionId, adapterConfig, regions } = renderProps;
+    const { dataAdapter } = await getAdapter(pluginManager, sessionId, adapterConfig);
+    const region = regions[0];
+    const features = await firstValueFrom(dataAdapter
+        .getFeatures(region, renderProps)
+        .pipe(toArray()));
+    return renderFeatures(renderProps, features);
+}

package/esm/saveTrackFormats/bedGraph.d.ts

@@ -0,0 +1,4 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function stringifyBedGraph({ features }: {
+    features: Feature[];
+}): string;

package/esm/saveTrackFormats/bedGraph.js

@@ -0,0 +1,11 @@
+export function stringifyBedGraph({ features }) {
+    return features
+        .map(feature => {
+        const chrom = feature.get('refName');
+        const start = feature.get('start');
+        const end = feature.get('end');
+        const score = feature.get('score') ?? 0;
+        return `${chrom}\t${start}\t${end}\t${score}`;
+    })
+        .join('\n');
+}

package/esm/shared/SharedWiggleConfigSchema.d.ts

@@ -1,8 +1,8 @@
-export default function sharedWiggleConfigFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function sharedWiggleConfigFactory(): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     autoscale: {
         type: string;
         defaultValue: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
+        model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         description: string;
     };
     minimalTicks: {
@@ -27,7 +27,7 @@ export default function sharedWiggleConfigFactory(): import("@jbrowse/core/confi
     };
     scaleType: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
+        model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
@@ -36,7 +36,7 @@ export default function sharedWiggleConfigFactory(): import("@jbrowse/core/confi
         description: string;
         defaultValue: boolean;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
         description: string;
@@ -63,4 +63,4 @@ export default function sharedWiggleConfigFactory(): import("@jbrowse/core/confi
         description: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/esm/shared/SharedWiggleConfigSchema.js

@@ -1,6 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from '@jbrowse/mobx-state-tree';
 import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
-import { types } from 'mobx-state-tree';
 export default function sharedWiggleConfigFactory() {
     return ConfigurationSchema('SharedWiggleDisplay', {
         autoscale: {