@jbrowse/plugin-wiggle 3.6.5 → 3.7.0

package/dist/MultiLinearWiggleDisplay/model.d.ts

@@ -195,6 +195,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
@@ -209,9 +210,22 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -220,6 +234,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -351,12 +366,14 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
         color: string;
         baseUri?: string;
         name: string;
+        source: string;
         group?: string;
     }[] | undefined;
     readonly sources: {
         color: string;
         baseUri?: string;
         name: string;
+        source: string;
         group?: string;
     }[] | undefined;
     readonly quantitativeStatsReady: boolean;

package/dist/MultiLinearWiggleDisplay/model.js

@@ -237,10 +237,10 @@ function stateModelFactory(_pluginManager, configSchema) {
     })
         .views(self => ({
         get legendFontSize() {
-            return Math.min(self.rowHeight, 12);
+            return Math.min(self.rowHeight, 8);
         },
         get canDisplayLegendLabels() {
-            return self.rowHeight > 11;
+            return self.rowHeight > 7;
         },
         get labelWidth() {
             var _a;

package/dist/MultiLinearWiggleDisplay/types.d.ts

@@ -6,6 +6,7 @@ export interface Source {
     group?: string;
     HP?: number;
     id?: string;
+    source: string;
     [key: string]: unknown;
 }
 export interface SampleInfo {

package/dist/MultiLinearWiggleDisplay/util.d.ts

@@ -1 +0,0 @@
-export declare function randomColor(str: string): string;

package/dist/MultiLinearWiggleDisplay/util.js

@@ -1,10 +1 @@
 "use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.randomColor = randomColor;
-function randomColor(str) {
-    let sum = 0;
-    for (let i = 0; i < str.length; i++) {
-        sum += str.charCodeAt(i);
-    }
-    return `hsl(${sum * 10}, 20%, 50%)`;
-}

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

@@ -8,6 +8,7 @@ interface WiggleOptions extends BaseOptions {
 interface AdapterEntry {
     dataAdapter: BaseFeatureDataAdapter;
     source: string;
+    name: string;
     [key: string]: unknown;
 }
 export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
@@ -24,7 +25,7 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
     }>;
     getSources(_regions: Region[]): Promise<{
         name: string;
-        __name: unknown;
+        source: string;
     }[]>;
 }
 export {};

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -9,6 +9,27 @@ function getFilename(uri) {
     const filename = uri.slice(uri.lastIndexOf('/') + 1);
     return filename.slice(0, filename.lastIndexOf('.'));
 }
+function getFilenameFromAdapterConfig(config) {
+    try {
+        if (config.type === 'BigWigAdapter' && config.bigWigLocation) {
+            const location = config.bigWigLocation;
+            if ('uri' in location && location.uri) {
+                return getFilename(location.uri);
+            }
+            if ('localPath' in location && location.localPath) {
+                return getFilename(location.localPath);
+            }
+            if ('blob' in location && location.blob) {
+                const blob = location.blob;
+                return blob.name ? getFilename(blob.name) : undefined;
+            }
+        }
+        return undefined;
+    }
+    catch (e) {
+        return undefined;
+    }
+}
 class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async getAdapters() {
         const getSubAdapter = this.getSubAdapter;
@@ -26,15 +47,20 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 },
             }));
         }
-        return Promise.all(subConfs.map(async (conf) => {
+        const ret = await Promise.all(subConfs.map(async (conf) => {
             const dataAdapter = (await getSubAdapter(conf))
                 .dataAdapter;
+            const source = conf.source ||
+                conf.name ||
+                getFilenameFromAdapterConfig(conf) ||
+                dataAdapter.id;
             return {
-                source: conf.name || dataAdapter.id,
                 ...conf,
                 dataAdapter,
+                source,
             };
         }));
+        return ret;
     }
     async getRefNames(opts) {
         const adapters = await this.getAdapters();
@@ -44,11 +70,9 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async getGlobalStats(opts) {
         const adapters = await this.getAdapters();
         const stats = (await Promise.all(adapters.map(adp => { var _a, _b; return (_b = (_a = adp.dataAdapter).getGlobalStats) === null || _b === void 0 ? void 0 : _b.call(_a, opts); }))).filter(f => !!f);
-        const scoreMin = (0, util_1.min)(stats.map(s => s.scoreMin));
-        const scoreMax = (0, util_1.max)(stats.map(s => s.scoreMax));
         return {
-            scoreMin,
-            scoreMax,
+            scoreMin: (0, util_1.min)(stats.map(s => s.scoreMin)),
+            scoreMax: (0, util_1.max)(stats.map(s => s.scoreMax)),
         };
     }
     getFeatures(region, opts = {}) {
@@ -70,11 +94,12 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getSources(_regions) {
         const adapters = await this.getAdapters();
-        return adapters.map(({ dataAdapter, source, name, ...rest }) => ({
-            name: source,
-            __name: name,
-            ...rest,
-        }));
+        return adapters.map(({ type, bigWigLocation, dataAdapter, ...rest }) => {
+            return {
+                ...rest,
+                name: rest.source,
+            };
+        });
     }
 }
 MultiWiggleAdapter.capabilities = [

package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js

@@ -71,7 +71,7 @@ function doSubmit({ trackName, val, model, }) {
 const MultiWiggleAddTrackWorkflow = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const [val, setVal] = (0, react_1.useState)('');
-    const [trackName, setTrackName] = (0, react_1.useState)(`MultiWiggle${+Date.now()}`);
+    const [trackName, setTrackName] = (0, react_1.useState)(`MultiWiggle${Date.now()}`);
     return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { className: classes.paper, children: [(0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsx)("li", { children: "Enter list of URLs for bigwig files in the textbox" }), (0, jsx_runtime_1.jsx)("li", { children: "Or, use the button below the text box to select files from your computer" })] }), (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, rows: 10, value: val, placeholder: "Paste list of URLs here, or use file selector below", variant: "outlined", onChange: event => {
                     setVal(event.target.value);
                 } }), (0, jsx_runtime_1.jsxs)(material_1.Button, { variant: "outlined", component: "label", children: ["Choose Files from your computer", (0, jsx_runtime_1.jsx)("input", { type: "file", hidden: true, multiple: true, onChange: ({ target }) => {

package/dist/getMultiWiggleSourcesAutorun.d.ts

@@ -1,6 +1,7 @@
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export interface Source {
     name: string;
+    source: string;
     color?: string;
     group?: string;
 }

package/dist/shared/SharedWiggleMixin.d.ts

@@ -187,6 +187,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
@@ -201,9 +202,22 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -212,6 +226,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/dist/util.d.ts

@@ -9,6 +9,7 @@ export interface ScaleOpts {
 export interface Source {
     baseUri?: string;
     name: string;
+    source: string;
     color?: string;
     group?: string;
 }

package/dist/util.js

@@ -84,7 +84,7 @@ function getNiceDomain({ scaleType, domain, bounds, }) {
     return scale.domain();
 }
 function toP(s = 0) {
-    return +(+s).toPrecision(6);
+    return +s.toPrecision(6);
 }
 function round(value) {
     return Math.round(value * 1e5) / 1e5;

package/esm/CreateMultiWiggleExtension/ConfirmDialog.js

@@ -4,7 +4,7 @@ import { readConfObject } from '@jbrowse/core/configuration';
 import Dialog from '@jbrowse/core/ui/Dialog';
 import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 const ConfirmDialog = ({ tracks, onClose, }) => {
-    const [val, setVal] = useState(`MultiWiggle ${Date.now()}`);
+    const [val, setVal] = useState(() => `MultiWiggle ${Date.now()}`);
     const allQuant = tracks.every(t => t.type === 'QuantitativeTrack');
     return (_jsxs(Dialog, { open: true, onClose: () => {
             onClose(false);

package/esm/CreateMultiWiggleExtension/index.js

@@ -8,7 +8,7 @@ function makeTrack({ model, arg, }) {
     const subadapters = tracks
         .map(c => readConfObject(c, 'adapter'))
         .map((c, idx) => ({ ...c, source: trackIds[idx] }));
-    const now = +Date.now();
+    const now = Date.now();
     const trackId = `multitrack-${now}-sessionTrack`;
     const session = getSession(model);
     if (isSessionWithAddTracks(session)) {

package/esm/LinearWiggleDisplay/model.d.ts

@@ -193,6 +193,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -207,9 +208,22 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -218,6 +232,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/esm/MultiLinearWiggleDisplay/components/ColorLegend.js

@@ -1,6 +1,7 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { observer } from 'mobx-react';
 import LegendItem from './LegendItem';
+import LegendItemText from './LegendItemText';
 import RectBg from './RectBg';
 const ColorLegend = observer(function ({ model, rowHeight, exportSVG, }) {
     const { graphType, needsFullHeightScalebar, rowHeightTooSmallForScalebar, renderColorBoxes, sources, labelWidth, } = model;
@@ -8,6 +9,6 @@ const ColorLegend = observer(function ({ model, rowHeight, exportSVG, }) {
     const legendWidth = labelWidth + colorBoxWidth + 5;
     const svgOffset = exportSVG ? 10 : 0;
     const extraOffset = svgOffset || (graphType && !rowHeightTooSmallForScalebar ? 50 : 0);
-    return sources ? (_jsxs(_Fragment, { children: [needsFullHeightScalebar ? (_jsx(RectBg, { y: 0, x: extraOffset, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null, sources.map((source, idx) => (_jsx(LegendItem, { source: source, idx: idx, model: model, rowHeight: rowHeight, exportSVG: exportSVG, labelWidth: labelWidth }, `${source.name}-${idx}`)))] })) : null;
+    return sources ? (_jsxs(_Fragment, { children: [needsFullHeightScalebar ? (_jsx(RectBg, { y: 0, x: extraOffset, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null, sources.map((source, idx) => (_jsx(LegendItem, { source: source, idx: idx, model: model, rowHeight: rowHeight, exportSVG: exportSVG, labelWidth: labelWidth }, `${source.name}-${idx}`))), sources.map((source, idx) => (_jsx(LegendItemText, { source: source, idx: idx, model: model, rowHeight: rowHeight, exportSVG: exportSVG }, `${source.name}-text-${idx}`)))] })) : null;
 });
 export default ColorLegend;

package/esm/MultiLinearWiggleDisplay/components/LegendItem.js

@@ -3,12 +3,10 @@ import RectBg from './RectBg';
 const LegendItem = function ({ source, idx, rowHeight, labelWidth, model, exportSVG, }) {
     const boxHeight = Math.min(20, rowHeight);
     const { needsCustomLegend, graphType, needsFullHeightScalebar, rowHeightTooSmallForScalebar, renderColorBoxes, } = model;
-    const svgFontSize = Math.min(rowHeight, 12);
-    const canDisplayLabel = rowHeight > 11;
     const colorBoxWidth = renderColorBoxes ? 15 : 0;
     const legendWidth = labelWidth + colorBoxWidth + 5;
     const svgOffset = exportSVG ? 10 : 0;
     const extraOffset = svgOffset || (graphType && !rowHeightTooSmallForScalebar ? 50 : 0);
-    return (_jsxs(_Fragment, { children: [needsFullHeightScalebar ? null : (_jsx(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: legendWidth, height: boxHeight })), source.color ? (_jsx(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: colorBoxWidth, height: needsCustomLegend ? rowHeight : boxHeight, color: source.color })) : null, canDisplayLabel ? (_jsx("text", { y: idx * rowHeight + 13, x: extraOffset + colorBoxWidth + 2, fontSize: svgFontSize, children: source.name })) : null] }));
+    return (_jsxs(_Fragment, { children: [needsFullHeightScalebar ? null : (_jsx(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: legendWidth, height: boxHeight })), source.color ? (_jsx(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: colorBoxWidth, height: needsCustomLegend ? rowHeight : boxHeight, color: source.color })) : null] }));
 };
 export default LegendItem;

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

@@ -0,0 +1,10 @@
+import type { Source } from '../../util';
+import type { WiggleDisplayModel } from '../model';
+declare const LegendItemText: ({ source, idx, rowHeight, model, exportSVG, }: {
+    source: Source;
+    idx: number;
+    rowHeight: number;
+    model: WiggleDisplayModel;
+    exportSVG?: boolean;
+}) => import("react/jsx-runtime").JSX.Element | null;
+export default LegendItemText;

package/esm/MultiLinearWiggleDisplay/components/LegendItemText.js

@@ -0,0 +1,11 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+const LegendItemText = function ({ source, idx, rowHeight, model, exportSVG, }) {
+    const { graphType, rowHeightTooSmallForScalebar, renderColorBoxes } = model;
+    const svgFontSize = Math.min(rowHeight, 12);
+    const canDisplayLabel = rowHeight >= 6;
+    const colorBoxWidth = renderColorBoxes ? 15 : 0;
+    const svgOffset = exportSVG ? 10 : 0;
+    const extraOffset = svgOffset || (graphType && !rowHeightTooSmallForScalebar ? 50 : 0);
+    return canDisplayLabel ? (_jsx("text", { y: idx * rowHeight + 13, x: extraOffset + colorBoxWidth + 2, fontSize: svgFontSize, children: source.name })) : null;
+};
+export default LegendItemText;

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js

@@ -1,36 +1,6 @@
-import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
-import { useState } from 'react';
-import DraggableDialog from '@jbrowse/core/ui/DraggableDialog';
-import { useLocalStorage } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
+import { jsx as _jsx } from "react/jsx-runtime";
 import SourcesGrid from './SourcesGrid';
-const useStyles = makeStyles()({
-    content: {
-        minWidth: 800,
-    },
-    float: {
-        float: 'right',
-    },
-});
-function HelpfulTips() {
-    return (_jsxs(_Fragment, { children: ["Helpful tips", _jsxs("ul", { children: [_jsx("li", { children: "You can select rows in the table with the checkboxes" }), _jsx("li", { children: "Multi-select is enabled with shift-click and control-click" }), _jsx("li", { children: "The \"Move selected items up/down\" can re-arrange subtracks" }), _jsx("li", { children: "Sorting the data grid itself can also re-arrange subtracks" }), _jsx("li", { children: "Changes are applied when you hit Submit" }), _jsx("li", { children: "You can click and drag the dialog box to move it on the screen" }), _jsx("li", { children: "Columns in the table can be hidden using a vertical '...' menu on the right side of each column" })] })] }));
-}
+import SharedSetColorDialog from './ui/SetColorDialog';
 export default function SetColorDialog({ model, handleClose, }) {
-    const { classes } = useStyles();
-    const { sources } = model;
-    const [currLayout, setCurrLayout] = useState(structuredClone(sources || []));
-    const [showTips, setShowTips] = useLocalStorage('multiwiggle-showTips', false);
-    return (_jsxs(DraggableDialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Multi-wiggle color/arrangement editor", children: [_jsxs(DialogContent, { className: classes.content, children: [_jsx(Button, { variant: "contained", className: classes.float, onClick: () => {
-                            setShowTips(!showTips);
-                        }, children: showTips ? 'Hide tips' : 'Show tips' }), _jsx("br", {}), showTips ? _jsx(HelpfulTips, {}) : null, _jsx(SourcesGrid, { rows: currLayout, onChange: setCurrLayout, showTips: showTips })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", type: "submit", color: "inherit", onClick: () => {
-                            model.clearLayout();
-                            setCurrLayout(model.sources || []);
-                        }, children: "Clear custom settings" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                            setCurrLayout([...(model.sources || [])]);
-                        }, children: "Cancel" }), _jsx(Button, { variant: "contained", color: "primary", type: "submit", onClick: () => {
-                            model.setLayout(currLayout);
-                            handleClose();
-                        }, children: "Submit" })] })] }));
+    return (_jsx(SharedSetColorDialog, { model: model, handleClose: handleClose, title: "Multi-wiggle color/arrangement editor", enableBulkEdit: true, enableRowPalettizer: true, showTipsStorageKey: "multiwiggle-showTips", SourcesGridComponent: SourcesGrid }));
 }

package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.js

@@ -22,7 +22,7 @@ function SourcesGrid({ rows, onChange, showTips, }) {
     const { classes } = useStyles();
     const [anchorEl, setAnchorEl] = useState(null);
     const [selected, setSelected] = useState([]);
-    const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0];
+    const { name: _name, color: _color, source: _source, baseUri: _baseUri, ...rest } = rows.length > 0 ? rows[0] : {};
     const [widgetColor, setWidgetColor] = useState('blue');
     const [currSort, setCurrSort] = useState({
         idx: 0,

package/esm/MultiLinearWiggleDisplay/components/Tooltip.js

@@ -13,15 +13,19 @@ const TooltipContents = forwardRef(function TooltipContents2({ model, feature },
     const source = feature.get('source');
     const summary = feature.get('summary');
     const obj = Object.fromEntries(model.sources.map(ent => [ent.name, ent]));
-    return (_jsxs("div", { ref: ref, children: [[refName, coord].filter(f => !!f).join(':'), _jsx("br", {}), sources ? (_jsxs("table", { children: [_jsx("thead", { children: _jsxs("tr", { children: [_jsx("th", { children: "color" }), _jsx("th", { children: "source" }), _jsx("th", { children: "score" })] }) }), _jsx("tbody", { children: Object.entries(sources).map(([source, data]) => (_jsxs("tr", { children: [_jsx("td", { children: _jsx("div", { style: {
-                                            width: 16,
-                                            height: 16,
-                                            background: obj[source].color,
-                                        } }) }), _jsx("td", { children: source }), _jsx("td", { children: toP(data.score) })] }, source))) })] })) : (_jsxs("span", { children: [source, ' ', summary
+    const obj2 = obj[source];
+    return (_jsxs("div", { ref: ref, children: [[refName, coord].filter(f => !!f).join(':'), _jsx("br", {}), sources ? (_jsxs("table", { children: [_jsx("thead", { children: _jsxs("tr", { children: [_jsx("th", { children: "color" }), _jsx("th", { children: "source" }), _jsx("th", { children: "score" })] }) }), _jsx("tbody", { children: Object.entries(sources).map(([source, data]) => {
+                            const sourceInfo = obj[source];
+                            return (_jsxs("tr", { children: [_jsx("td", { children: sourceInfo && (_jsx("div", { style: {
+                                                width: 16,
+                                                height: 16,
+                                                background: sourceInfo.color,
+                                            } })) }), _jsx("td", { children: (sourceInfo === null || sourceInfo === void 0 ? void 0 : sourceInfo.name) || source }), _jsx("td", { children: toP(data.score) })] }, source));
+                        }) })] })) : (_jsxs("span", { children: [(obj2 === null || obj2 === void 0 ? void 0 : obj2.name) || source, ' ', summary
                         ? `min:${toP(feature.get('minScore'))} avg:${toP(feature.get('score'))} max:${toP(feature.get('maxScore'))}`
                         : toP(feature.get('score'))] }))] }));
 });
-const WiggleTooltip = observer((props) => {
+const WiggleTooltip = observer(function (props) {
     return _jsx(Tooltip, { useClientY: true, TooltipContents: TooltipContents, ...props });
 });
 export default WiggleTooltip;

package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.js

@@ -21,6 +21,7 @@ const WiggleClusterDialogAuto = observer(function ({ model, children, handleClos
                                         } })] })) : null] }), _jsxs("div", { children: [loading ? (_jsxs("div", { style: { padding: 50 }, children: [_jsx("span", { children: progress || 'Loading...' }), _jsx(Button, { onClick: () => {
                                             stopStopToken(stopToken);
                                         }, children: "Stop" })] })) : null, error ? _jsx(ErrorMessage, { error: error }) : null] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", disabled: loading, onClick: async () => {
+                            var _a;
                             try {
                                 setError(undefined);
                                 setProgress('Initializing');
@@ -46,12 +47,19 @@ const WiggleClusterDialogAuto = observer(function ({ model, children, handleClos
                                             setProgress(arg);
                                         },
                                     }));
+                                    const currentLayout = ((_a = model.layout) === null || _a === void 0 ? void 0 : _a.length)
+                                        ? model.layout
+                                        : sourcesWithoutLayout;
+                                    const sourcesByName = Object.fromEntries(currentLayout.map((s) => [s.name, s]));
                                     model.setLayout(ret.order.map(idx => {
-                                        const ret = sourcesWithoutLayout[idx];
-                                        if (!ret) {
+                                        const sourceItem = sourcesWithoutLayout[idx];
+                                        if (!sourceItem) {
                                             throw new Error(`out of bounds at ${idx}`);
                                         }
-                                        return ret;
+                                        return {
+                                            ...sourceItem,
+                                            ...sourcesByName[sourceItem.name],
+                                        };
                                     }));
                                 }
                                 handleClose();

package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.js

@@ -61,7 +61,7 @@ const WiggleClusterDialogManuals = observer(function ({ model, handleClose, chil
         })();
     }, [model, samplesPerPixel]);
     const results = ret
-        ? `inputMatrix<-matrix(c(${Object.values(ret)
+        ? String.raw `inputMatrix<-matrix(c(${Object.values(ret)
             .map(val => val.join(','))
             .join(',\n')}
 ),nrow=${Object.values(ret).length},byrow=TRUE)
@@ -69,7 +69,7 @@ rownames(inputMatrix)<-c(${Object.keys(ret)
             .map(key => `'${key}'`)
             .join(',')})
 resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
-cat(resultClusters$order,sep='\\n')`
+cat(resultClusters$order,sep='\n')`
         : undefined;
     const resultsTsv = ret
         ? Object.entries(ret)
@@ -102,7 +102,7 @@ cat(resultClusters$order,sep='\\n')`
                                                             setClusterMethod(key);
                                                         } }), label: val }, key))) }), _jsxs("div", { style: { marginTop: 20 }, children: [_jsx(Typography, { children: "This procedure samples the data at each 'pixel' across the visible by default" }), _jsx(TextField, { label: "Samples per pixel (>1 for denser sampling, between 0-1 for sparser sampling)", variant: "outlined", size: "small", value: samplesPerPixel, onChange: event => {
                                                             setSamplesPerPixel(event.target.value);
-                                                        } })] })] })) : null, results ? (_jsx("div", {})) : loading ? (_jsx(LoadingEllipses, { variant: "h6", title: "Generating score matrix" })) : error ? (_jsx(ErrorMessage, { error: error })) : null] }), _jsxs("div", { children: [_jsx(Typography, { variant: "subtitle2", gutterBottom: true, style: { marginTop: '16px' }, children: "Clustering Results:" }), _jsx(TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
+                                                        } })] })] })) : null, results ? (_jsx("div", {})) : loading ? (_jsx(LoadingEllipses, { variant: "h6", message: "Generating score matrix" })) : error ? (_jsx(ErrorMessage, { error: error })) : null] }), _jsxs("div", { children: [_jsx(Typography, { variant: "subtitle2", gutterBottom: true, style: { marginTop: '16px' }, children: "Clustering Results:" }), _jsx(TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "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: {
@@ -111,20 +111,28 @@ cat(resultClusters$order,sep='\\n')`
                                                 },
                                             },
                                         } })] })] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", onClick: () => {
+                            var _a;
                             const { sourcesWithoutLayout } = model;
                             if (sourcesWithoutLayout) {
                                 try {
+                                    const currentLayout = ((_a = model.layout) === null || _a === void 0 ? void 0 : _a.length)
+                                        ? model.layout
+                                        : sourcesWithoutLayout;
+                                    const sourcesByName = Object.fromEntries(currentLayout.map((s) => [s.name, s]));
                                     model.setLayout(paste
                                         .split('\n')
                                         .map(t => t.trim())
                                         .filter(f => !!f)
                                         .map(r => +r)
                                         .map(idx => {
-                                        const ret = sourcesWithoutLayout[idx - 1];
-                                        if (!ret) {
+                                        const sourceItem = sourcesWithoutLayout[idx - 1];
+                                        if (!sourceItem) {
                                             throw new Error(`out of bounds at ${idx}`);
                                         }
-                                        return ret;
+                                        return {
+                                            ...sourceItem,
+                                            ...sourcesByName[sourceItem.name],
+                                        };
                                     }));
                                 }
                                 catch (e) {

package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.d.ts

@@ -1,7 +1,8 @@
-import type { Source } from '../../types';
+import type { Source } from '../../../util';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export interface ReducedModel {
     sourcesWithoutLayout?: Source[];
+    layout?: Source[];
     adapterConfig: AnyConfigurationModel;
     setLayout: (arg: Source[]) => void;
 }

package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialog.d.ts

@@ -0,0 +1,31 @@
+interface SetColorDialogProps {
+    model: {
+        sources?: {
+            name: string;
+            [key: string]: unknown;
+        }[];
+        setLayout: (s: {
+            name: string;
+            [key: string]: unknown;
+        }[]) => void;
+        clearLayout: () => void;
+    };
+    handleClose: () => void;
+    title?: string;
+    enableBulkEdit?: boolean;
+    enableRowPalettizer?: boolean;
+    showTipsStorageKey?: string;
+    SourcesGridComponent: React.ComponentType<{
+        rows: {
+            name: string;
+            [key: string]: unknown;
+        }[];
+        onChange: (rows: {
+            name: string;
+            [key: string]: unknown;
+        }[]) => void;
+        showTips: boolean;
+    }>;
+}
+export default function SetColorDialog({ model, handleClose, title, enableBulkEdit, enableRowPalettizer, showTipsStorageKey, SourcesGridComponent, }: SetColorDialogProps): import("react/jsx-runtime").JSX.Element;
+export {};