@jbrowse/plugin-wiggle 3.1.0 → 3.3.0

package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.js

@@ -1,47 +1,15 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { groupBy } from '@jbrowse/core/util';
-import { firstValueFrom, toArray } from 'rxjs';
+import { getScoreMatrix } from './getScoreMatrix';
 export class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
         super(...arguments);
         this.name = 'MultiWiggleGetScoreMatrix';
     }
     async execute(args, rpcDriverClassName) {
-        var _a, _b;
-        const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { sources, regions, adapterConfig, sessionId, bpPerPx } = deserializedArgs;
-        const adapter = await getAdapter(pm, sessionId, adapterConfig);
-        const dataAdapter = adapter.dataAdapter;
-        const resolution = 2;
-        const bpScale = bpPerPx / resolution;
-        const r0 = regions[0];
-        const r0len = r0.end - r0.start;
-        const w = Math.floor(r0len / bpScale);
-        const feats = await firstValueFrom(dataAdapter.getFeatures(r0, deserializedArgs).pipe(toArray()));
-        const groups = groupBy(feats, f => f.get('source'));
-        const rows = {};
-        for (const source of sources) {
-            const { name } = source;
-            const features = groups[name] || [];
-            for (const feat of features) {
-                if (!rows[name]) {
-                    rows[name] = {
-                        name,
-                        scores: new Array(w),
-                    };
-                }
-                const fstart = feat.get('start');
-                const fend = feat.get('end');
-                const score = feat.get('score');
-                for (let i = fstart; i < fend; i += bpScale) {
-                    if (i > r0.start && i < r0.end) {
-                        (_a = rows[name].scores)[_b = Math.floor((i - r0.start) / bpScale)] || (_a[_b] = score);
-                    }
-                }
-            }
-        }
-        return rows;
+        return getScoreMatrix({
+            args: deserializedArgs,
+            pluginManager: this.pluginManager,
+        });
     }
 }

package/esm/WiggleRPC/getScoreMatrix.d.ts

@@ -0,0 +1,6 @@
+import type { GetScoreMatrixArgs } from './types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function getScoreMatrix({ pluginManager, args, }: {
+    args: GetScoreMatrixArgs;
+    pluginManager: PluginManager;
+}): Promise<Record<string, number[]>>;

package/esm/WiggleRPC/getScoreMatrix.js

@@ -0,0 +1,32 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { groupBy } from '@jbrowse/core/util';
+import { firstValueFrom, toArray } from 'rxjs';
+export async function getScoreMatrix({ pluginManager, args, }) {
+    const { sources, regions, adapterConfig, sessionId, bpPerPx } = args;
+    const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
+    const dataAdapter = adapter.dataAdapter;
+    const r0 = regions[0];
+    const r0len = r0.end - r0.start;
+    const w = Math.floor(r0len / bpPerPx);
+    const feats = await firstValueFrom(dataAdapter.getFeatures(r0, args).pipe(toArray()));
+    const groups = groupBy(feats, f => f.get('source'));
+    const rows = {};
+    for (const source of sources) {
+        const { name } = source;
+        const features = groups[name] || [];
+        const arr = new Array(w).fill(0);
+        for (const feat of features) {
+            const fstart = feat.get('start');
+            const fend = feat.get('end');
+            const score = feat.get('score');
+            for (let i = fstart; i < fend; i += bpPerPx) {
+                const x = Math.floor((i - r0.start) / bpPerPx);
+                if (x >= 0 && x < w) {
+                    arr[x] || (arr[x] = score);
+                }
+            }
+        }
+        rows[name] = arr;
+    }
+    return rows;
+}

package/esm/WiggleRPC/rpcMethods.d.ts

@@ -2,3 +2,4 @@ export * from './MultiWiggleGetSources';
 export * from './WiggleGetMultiRegionQuantitativeStats';
 export * from './WiggleGetGlobalQuantitativeStats';
 export * from './MultiWiggleGetScoreMatrix';
+export * from './MultiWiggleClusterScoreMatrix';

package/esm/WiggleRPC/rpcMethods.js

@@ -2,3 +2,4 @@ export * from './MultiWiggleGetSources';
 export * from './WiggleGetMultiRegionQuantitativeStats';
 export * from './WiggleGetGlobalQuantitativeStats';
 export * from './MultiWiggleGetScoreMatrix';
+export * from './MultiWiggleClusterScoreMatrix';

package/esm/WiggleRPC/type.js

@@ -0,0 +1 @@
+"use strict";

package/esm/WiggleRPC/types.d.ts

@@ -0,0 +1,13 @@
+import type { Source } from '../util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export interface GetScoreMatrixArgs {
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    sources: Source[];
+    statusCallback?: (arg: string) => void;
+}

package/esm/WiggleRPC/types.js

@@ -0,0 +1 @@
+export {};

package/esm/drawDensity.d.ts

@@ -12,6 +12,7 @@ export declare function drawDensity(ctx: CanvasRenderingContext2D, props: {
     };
     displayCrossHatches: boolean;
     config: AnyConfigurationModel;
+    stopToken?: string;
 }): {
     reducedFeatures: Feature[];
 };

package/esm/drawDensity.js

@@ -1,10 +1,11 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { featureSpanPx } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { fillRectCtx, getScale } from './util';
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 export function drawDensity(ctx, props) {
-    const { features, regions, bpPerPx, scaleOpts, height, config } = props;
+    const { stopToken, features, regions, bpPerPx, scaleOpts, height, config } = props;
     const region = regions[0];
     const pivot = readConfObject(config, 'bicolorPivot');
     const pivotValue = readConfObject(config, 'bicolorPivotValue');
@@ -16,7 +17,7 @@ export function drawDensity(ctx, props) {
     const scale = getScale({
         ...scaleOpts,
         pivotValue: crossing ? pivotValue : undefined,
-        range: crossing ? [negColor, 'white', posColor] : ['white', posColor],
+        range: crossing ? [negColor, '#eee', posColor] : ['#eee', posColor],
     });
     const scale2 = getScale({ ...scaleOpts, range: [0, height] });
     const cb = color === '#f0f'
@@ -28,7 +29,12 @@ export function drawDensity(ctx, props) {
     let prevLeftPx = Number.NEGATIVE_INFINITY;
     let hasClipping = false;
     const reducedFeatures = [];
+    let start = performance.now();
     for (const feature of features.values()) {
+        if (performance.now() - start > 400) {
+            checkStopToken(stopToken);
+            start = performance.now();
+        }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
             reducedFeatures.push(feature);
@@ -44,6 +50,10 @@ export function drawDensity(ctx, props) {
     if (hasClipping) {
         ctx.fillStyle = clipColor;
         for (const feature of features.values()) {
+            if (performance.now() - start > 400) {
+                checkStopToken(stopToken);
+                start = performance.now();
+            }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
             const w = rightPx - leftPx + fudgeFactor;
             const score = feature.get('score');

package/esm/drawLine.d.ts

@@ -14,6 +14,7 @@ export declare function drawLine(ctx: CanvasRenderingContext2D, props: {
     colorCallback: (f: Feature, score: number) => string;
     config: AnyConfigurationModel;
     offset?: number;
+    stopToken?: string;
 }): {
     reducedFeatures: Feature[];
 };

package/esm/drawLine.js

@@ -1,10 +1,11 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { clamp, featureSpanPx } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { getScale } from './util';
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 export function drawLine(ctx, props) {
-    const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, } = props;
+    const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, stopToken, } = props;
     const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
     const height = unadjustedHeight - offset * 2;
@@ -17,7 +18,12 @@ export function drawLine(ctx, props) {
     let lastVal;
     let prevLeftPx = Number.NEGATIVE_INFINITY;
     const reducedFeatures = [];
+    let start = performance.now();
     for (const feature of features.values()) {
+        if (performance.now() - start > 400) {
+            checkStopToken(stopToken);
+            start = performance.now();
+        }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
             reducedFeatures.push(feature);
@@ -55,12 +61,12 @@ export function drawLine(ctx, props) {
     if (displayCrossHatches) {
         ctx.lineWidth = 1;
         ctx.strokeStyle = 'rgba(200,200,200,0.5)';
-        values.forEach(tick => {
+        for (const tick of values) {
             ctx.beginPath();
             ctx.moveTo(0, Math.round(toY(tick)));
             ctx.lineTo(width, Math.round(toY(tick)));
             ctx.stroke();
-        });
+        }
     }
     return { reducedFeatures };
 }

package/esm/drawXY.js

@@ -22,7 +22,7 @@ function darken(color, amount) {
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 export function drawXY(ctx, props) {
-    const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, inverted, } = props;
+    const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, inverted, stopToken, } = props;
     const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
     const height = unadjustedHeight - offset * 2;
@@ -50,7 +50,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -72,7 +72,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -102,7 +102,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -124,7 +124,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -155,7 +155,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -173,12 +173,12 @@ export function drawXY(ctx, props) {
     if (displayCrossHatches) {
         ctx.lineWidth = 1;
         ctx.strokeStyle = 'rgba(200,200,200,0.5)';
-        ticks.values.forEach(tick => {
+        for (const tick of ticks.values) {
             ctx.beginPath();
             ctx.moveTo(0, Math.round(toY(tick)));
             ctx.lineTo(width, Math.round(toY(tick)));
             ctx.stroke();
-        });
+        }
     }
     return { reducedFeatures };
 }

package/esm/index.js

@@ -16,7 +16,7 @@ import MultiWiggleAddTrackWorkflowF from './MultiWiggleAddTrackWorkflow';
 import MultiXYPlotRendererF from './MultiXYPlotRenderer';
 import QuantitativeTrackF from './QuantitativeTrack';
 import WiggleBaseRenderer from './WiggleBaseRenderer';
-import { MultiWiggleGetScoreMatrix, MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from './WiggleRPC/rpcMethods';
+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';
 export default class WigglePlugin extends Plugin {
@@ -55,6 +55,7 @@ export default class WigglePlugin extends Plugin {
         pm.addRpcMethod(() => new WiggleGetMultiRegionQuantitativeStats(pm));
         pm.addRpcMethod(() => new MultiWiggleGetSources(pm));
         pm.addRpcMethod(() => new MultiWiggleGetScoreMatrix(pm));
+        pm.addRpcMethod(() => new MultiWiggleClusterScoreMatrix(pm));
     }
 }
 export * from './util';

package/esm/shared/SharedWiggleMixin.d.ts

@@ -252,11 +252,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     setCrossHatches(cross: boolean): void;
 } & {
     readonly adapterTypeName: any;
-    readonly rendererTypeNameSimple: any;
+    readonly rendererTypeNameSimple: string;
     readonly filters: undefined;
-    readonly scaleType: any;
-    readonly maxScore: any;
-    readonly minScore: any;
+    readonly scaleType: string;
+    readonly maxScore: number;
+    readonly minScore: number;
 } & {
     readonly adapterCapabilities: string[];
     readonly rendererConfig: {
@@ -270,7 +270,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
-    readonly autoscaleType: any;
+    readonly autoscaleType: string;
 } & {
     readonly domain: number[] | undefined;
 } & {
@@ -283,9 +283,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             scoreMin: number;
             scoreMax: number;
         } | undefined;
-        autoscaleType: any;
-        scaleType: any;
-        inverted: any;
+        autoscaleType: string;
+        scaleType: string;
+        inverted: boolean;
     };
     readonly canHaveFill: boolean;
     readonly displayCrossHatchesSetting: boolean;

package/esm/shared/SharedWiggleMixin.js

@@ -118,7 +118,7 @@ export default function SharedWiggleMixin(configSchema) {
         },
         get rendererTypeNameSimple() {
             var _a;
-            return (_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : getConf(self, 'defaultRendering');
+            return ((_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : getConf(self, 'defaultRendering'));
         },
         get filters() {
             return undefined;
@@ -189,12 +189,12 @@ export default function SharedWiggleMixin(configSchema) {
     })
         .views(self => ({
         get filled() {
-            const { fill, rendererConfig } = self;
-            return fill !== null && fill !== void 0 ? fill : readConfObject(rendererConfig, 'filled');
+            var _a;
+            return ((_a = self.fill) !== null && _a !== void 0 ? _a : readConfObject(self.rendererConfig, 'filled'));
         },
         get summaryScoreModeSetting() {
-            const { summaryScoreMode: mode, rendererConfig } = self;
-            return mode !== null && mode !== void 0 ? mode : readConfObject(rendererConfig, 'summaryScoreMode');
+            var _a;
+            return ((_a = self.summaryScoreMode) !== null && _a !== void 0 ? _a : readConfObject(self.rendererConfig, 'summaryScoreMode'));
         },
         get scaleOpts() {
             return {
@@ -209,8 +209,8 @@ export default function SharedWiggleMixin(configSchema) {
             return self.rendererTypeName === 'XYPlotRenderer';
         },
         get displayCrossHatchesSetting() {
-            const { displayCrossHatches: hatches, rendererConfig } = self;
-            return hatches !== null && hatches !== void 0 ? hatches : readConfObject(rendererConfig, 'displayCrossHatches');
+            var _a;
+            return ((_a = self.displayCrossHatches) !== null && _a !== void 0 ? _a : readConfObject(self.rendererConfig, 'displayCrossHatches'));
         },
         get hasResolution() {
             return self.adapterCapabilities.includes('hasResolution');
@@ -285,7 +285,10 @@ export default function SharedWiggleMixin(configSchema) {
                     onClick: () => {
                         getSession(self).queueDialog(handleClose => [
                             SetMinMaxDialog,
-                            { model: self, handleClose },
+                            {
+                                model: self,
+                                handleClose,
+                            },
                         ]);
                     },
                 },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "3.1.0",
+  "version": "3.3.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,13 +37,13 @@
   },
   "dependencies": {
     "@gmod/bbi": "^6.0.0",
-    "@jbrowse/core": "^3.1.0",
-    "@jbrowse/plugin-data-management": "^3.1.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.1.0",
-    "@mui/icons-material": "^6.0.0",
-    "@mui/material": "^6.0.0",
-    "@mui/x-charts-vendor": "^7.12.0",
-    "@mui/x-data-grid": "^7.0.0",
+    "@jbrowse/core": "^3.3.0",
+    "@jbrowse/plugin-data-management": "^3.3.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.3.0",
+    "@mui/icons-material": "^7.0.0",
+    "@mui/material": "^7.0.0",
+    "@mui/x-charts-vendor": "^8.0.0",
+    "@mui/x-data-grid": "^8.0.0",
     "fast-deep-equal": "^3.1.3",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
@@ -62,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
 }

package/dist/MultiLinearWiggleDisplay/components/ClusterDialog.d.ts

@@ -1,11 +0,0 @@
-import type { Source } from '../types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export default function ClusterDialog({ model, handleClose, }: {
-    model: {
-        sources?: Source[];
-        minorAlleleFrequencyFilter?: number;
-        adapterConfig: AnyConfigurationModel;
-        setLayout: (arg: Source[]) => void;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/MultiLinearWiggleDisplay/components/ClusterDialog.js

@@ -1,115 +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 = ClusterDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const material_1 = require("@mui/material");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const file_saver_1 = require("file-saver");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-    mgap: {
-        display: 'flex',
-        flexDirection: 'column',
-        gap: theme.spacing(4),
-    },
-}));
-function ClusterDialog({ model, handleClose, }) {
-    const { classes } = useStyles();
-    const [results, setResults] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    const [paste, setPaste] = (0, react_1.useState)('');
-    const [useCompleteMethod, setUseCompleteMethod] = (0, react_1.useState)(false);
-    (0, react_1.useEffect)(() => {
-        ;
-        (async () => {
-            try {
-                setError(undefined);
-                const view = (0, util_1.getContainingView)(model);
-                if (!view.initialized) {
-                    return;
-                }
-                const { rpcManager } = (0, util_1.getSession)(model);
-                const { sources, minorAlleleFrequencyFilter, adapterConfig } = model;
-                const sessionId = (0, tracks_1.getRpcSessionId)(model);
-                const { bpPerPx } = view;
-                const ret = (await rpcManager.call(sessionId, 'MultiWiggleGetScoreMatrix', {
-                    regions: view.dynamicBlocks.contentBlocks,
-                    sources,
-                    minorAlleleFrequencyFilter,
-                    sessionId,
-                    adapterConfig,
-                    bpPerPx,
-                }));
-                const entries = Object.values(ret);
-                const keys = Object.keys(ret);
-                const clusterMethod = useCompleteMethod ? 'complete' : 'single';
-                const text = `try(library(fastcluster), silent=TRUE)
-inputMatrix<-matrix(c(${entries.map(val => val.scores.join(',')).join(',\n')}
-),nrow=${entries.length},byrow=TRUE)
-rownames(inputMatrix)<-c(${keys.map(key => `'${key}'`).join(',')})
-resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
-cat(resultClusters$order,sep='\\n')`;
-                setResults(text);
-            }
-            catch (e) {
-                if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(model)) {
-                    console.error(e);
-                    setError(e);
-                }
-            }
-        })();
-    }, [model, useCompleteMethod]);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Cluster by score", onClose: handleClose, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsxs)("div", { className: classes.mgap, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This page will produce an R script that will perform hierarchical clustering on the visible score data using `hclust`." }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "You can then paste the results in this form to specify the row ordering." }), results ? ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsxs)("div", { children: ["Step 1:", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                            (0, file_saver_1.saveAs)(new Blob([results || ''], {
-                                                type: 'text/plain;charset=utf-8',
-                                            }), 'cluster.R');
-                                        }, children: "Download Rscript" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                            (0, copy_to_clipboard_1.default)(results || '');
-                                        }, children: "Copy Rscript to clipboard" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: useCompleteMethod, onChange: e => {
-                                                setUseCompleteMethod(e.target.checked);
-                                            } }), label: "Use 'complete' linkage method instead of 'single'" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
-                                                setPaste(event.target.value);
-                                            }, slotProps: {
-                                                input: {
-                                                    classes: {
-                                                        input: classes.textAreaFont,
-                                                    },
-                                                },
-                                            } }) })] }) })) : ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { variant: "h6", title: "Generating score matrix" })), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null] }) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !results, variant: "contained", onClick: () => {
-                            const { sources } = model;
-                            if (sources) {
-                                try {
-                                    model.setLayout(paste
-                                        .split('\n')
-                                        .map(t => t.trim())
-                                        .filter(f => !!f)
-                                        .map(r => +r)
-                                        .map(idx => {
-                                        const ret = sources[idx - 1];
-                                        if (!ret) {
-                                            throw new Error(`out of bounds at ${idx}`);
-                                        }
-                                        return ret;
-                                    }));
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    setError(e);
-                                }
-                            }
-                            handleClose();
-                        }, children: "Apply clustering" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-}

package/esm/MultiLinearWiggleDisplay/components/ClusterDialog.d.ts

@@ -1,11 +0,0 @@
-import type { Source } from '../types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export default function ClusterDialog({ model, handleClose, }: {
-    model: {
-        sources?: Source[];
-        minorAlleleFrequencyFilter?: number;
-        adapterConfig: AnyConfigurationModel;
-        setLayout: (arg: Source[]) => void;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;