@jbrowse/plugin-wiggle 3.2.0 → 3.4.0

package/esm/MultiLinearWiggleDisplay/components/{ClusterDialog/ClusterDialog.js → WiggleClusterDialog/WiggleClusterDialog.js}

@@ -3,22 +3,22 @@ import { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { FormControlLabel, Radio, RadioGroup } from '@mui/material';
 import { observer } from 'mobx-react';
-import ClusterDialogAuto from './ClusterDialogAuto';
-import ClusterDialogManual from './ClusterDialogManual';
+import WiggleClusterDialogAuto from './WiggleClusterDialogAuto';
+import WiggleClusterDialogManual from './WiggleClusterDialogManual';
 function Header({ activeMode, setActiveMode, }) {
     return (_jsx("div", { children: _jsx(RadioGroup, { children: Object.entries({
-                auto: (_jsx("div", { children: "Run in-app clustering (slow for large data, built in JS clustering)" })),
-                manual: (_jsx("div", { children: "Download R script to run clustering (faster for large data, uses hclust, may be more accurate)" })),
+                auto: (_jsx("div", { children: "Run in-app clustering (slower, particularly for large numbers of samples, uses JS implementation of hclust)" })),
+                manual: (_jsx("div", { children: "Download R script to run clustering (faster, uses R implementation of hclust)" })),
             }).map(([key, val]) => (_jsx(FormControlLabel, { control: _jsx(Radio, { checked: activeMode === key, onChange: () => {
                         setActiveMode(key);
                     } }), label: val }, key))) }) }));
 }
-const ClusterDialog = observer(function ({ model, handleClose, }) {
+const WiggleClusterDialog = observer(function ({ model, handleClose, }) {
     const [activeMode, setActiveMode] = useState('auto');
     return (_jsx(Dialog, { open: true, title: "Cluster by score", maxWidth: "xl", onClose: (_, reason) => {
             if (reason !== 'backdropClick') {
                 handleClose();
             }
-        }, children: activeMode === 'auto' ? (_jsx(ClusterDialogAuto, { model: model, handleClose: handleClose, children: _jsx(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) : (_jsx(ClusterDialogManual, { model: model, handleClose: handleClose, children: _jsx(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) }));
+        }, children: activeMode === 'auto' ? (_jsx(WiggleClusterDialogAuto, { model: model, handleClose: handleClose, children: _jsx(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) : (_jsx(WiggleClusterDialogManual, { model: model, handleClose: handleClose, children: _jsx(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) }));
 });
-export default ClusterDialog;
+export default WiggleClusterDialog;

package/{dist/MultiLinearWiggleDisplay/components/ClusterDialog/ClusterDialogManual.d.ts → esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.d.ts}

@@ -1,7 +1,7 @@
 import type { ReducedModel } from './types';
-declare const ClusterDialogManuals: ({ model, handleClose, children, }: {
+declare const WiggleClusterDialogAuto: ({ model, children, handleClose, }: {
     model: ReducedModel;
-    handleClose: () => void;
     children: React.ReactNode;
+    handleClose: () => void;
 }) => import("react/jsx-runtime").JSX.Element;
-export default ClusterDialogManuals;
+export default WiggleClusterDialogAuto;

package/esm/MultiLinearWiggleDisplay/components/{ClusterDialog/ClusterDialogAuto.js → WiggleClusterDialog/WiggleClusterDialogAuto.js}

@@ -7,9 +7,10 @@ import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { isAlive } from 'mobx-state-tree';
-const ClusterDialogAuto = observer(function ({ model, children, handleClose, }) {
+const WiggleClusterDialogAuto = observer(function ({ model, children, handleClose, }) {
     const [progress, setProgress] = useState('');
     const [error, setError] = useState();
+    const [loading, setLoading] = useState(false);
     const [stopToken, setStopToken] = useState('');
     const [showAdvanced, setShowAdvanced] = useState(false);
     const [samplesPerPixel, setSamplesPerPixel] = useLocalStorage('cluster-samplesPerPixel', '1');
@@ -17,12 +18,13 @@ const ClusterDialogAuto = observer(function ({ model, children, handleClose, })
                                     setShowAdvanced(!showAdvanced);
                                 }, children: showAdvanced ? 'Hide advanced options' : 'Show advanced options' }), showAdvanced ? (_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] }), _jsxs("div", { children: [progress ? (_jsxs("div", { style: { padding: 50 }, children: [_jsxs("span", { style: { width: 400 }, children: ["Progress: ", progress] }), _jsx(Button, { onClick: () => {
+                                        } })] })) : 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", onClick: async () => {
+                                        }, children: "Stop" })] })) : null, error ? _jsx(ErrorMessage, { error: error }) : null] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", disabled: loading, onClick: async () => {
                             try {
                                 setError(undefined);
-                                setProgress('');
+                                setProgress('Initializing');
+                                setLoading(true);
                                 const view = getContainingView(model);
                                 if (!view.initialized) {
                                     return;
@@ -61,6 +63,7 @@ const ClusterDialogAuto = observer(function ({ model, children, handleClose, })
                                 }
                             }
                             finally {
+                                setLoading(false);
                                 setProgress('');
                                 setStopToken('');
                             }
@@ -71,4 +74,4 @@ const ClusterDialogAuto = observer(function ({ model, children, handleClose, })
                             }
                         }, children: "Cancel" })] })] }));
 });
-export default ClusterDialogAuto;
+export default WiggleClusterDialogAuto;

package/esm/MultiLinearWiggleDisplay/components/{ClusterDialog/ClusterDialogManual.d.ts → WiggleClusterDialog/WiggleClusterDialogManual.d.ts}

@@ -1,7 +1,7 @@
 import type { ReducedModel } from './types';
-declare const ClusterDialogManuals: ({ model, handleClose, children, }: {
+declare const WiggleClusterDialogManuals: ({ model, handleClose, children, }: {
     model: ReducedModel;
     handleClose: () => void;
     children: React.ReactNode;
 }) => import("react/jsx-runtime").JSX.Element;
-export default ClusterDialogManuals;
+export default WiggleClusterDialogManuals;

package/esm/MultiLinearWiggleDisplay/components/{ClusterDialog/ClusterDialogManual.js → WiggleClusterDialog/WiggleClusterDialogManual.js}

@@ -1,9 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { useEffect, useState } from 'react';
-import { CascadingMenuButton, ErrorMessage, LoadingEllipses, } from '@jbrowse/core/ui';
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 import { getContainingView, getSession, isAbortException, useLocalStorage, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import MenuIcon from '@mui/icons-material/Menu';
 import { Button, DialogActions, DialogContent, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
 import copy from 'copy-to-clipboard';
 import { saveAs } from 'file-saver';
@@ -20,15 +19,15 @@ const useStyles = makeStyles()(theme => ({
         gap: theme.spacing(4),
     },
 }));
-const ClusterDialogManuals = observer(function ({ model, handleClose, children, }) {
+const WiggleClusterDialogManuals = observer(function ({ model, handleClose, children, }) {
     const { classes } = useStyles();
     const [paste, setPaste] = useState('');
     const [ret, setRet] = useState();
     const [error, setError] = useState();
     const [loading, setLoading] = useState(false);
-    const [showAdvanced, setShowAdvanced] = useState(false);
-    const [clusterMethod, setClusterMethod] = useLocalStorage('cluster-clusterMethod', 'single');
-    const [samplesPerPixel, setSamplesPerPixel] = useLocalStorage('cluster-samplesPerPixel', '1');
+    const [showAdvanced, setShowAdvanced] = useLocalStorage('cluster-showAdvanced', false);
+    const [clusterMethod, setClusterMethod] = useState('single');
+    const [samplesPerPixel, setSamplesPerPixel] = useState('1');
     useEffect(() => {
         ;
         (async () => {
@@ -77,42 +76,33 @@ cat(resultClusters$order,sep='\\n')`
             .map(([key, val]) => [key, ...val].join('\t'))
             .join('\n')
         : undefined;
-    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [children, _jsxs("div", { style: { marginTop: 50 }, children: [_jsxs("div", { style: {
-                                    display: 'flex',
-                                    gap: '8px',
-                                    flexWrap: 'wrap',
-                                    marginBottom: '16px',
-                                }, children: [_jsx(Button, { variant: "contained", onClick: () => {
-                                            saveAs(new Blob([results || ''], {
-                                                type: 'text/plain;charset=utf-8',
-                                            }), 'cluster.R');
-                                        }, children: "Download Rscript" }), ' ', "or", ' ', _jsx(Button, { variant: "contained", onClick: () => {
-                                            copy(results || '');
-                                        }, children: "Copy Rscript to clipboard" }), ' ', _jsx("div", { style: { float: 'right' }, children: _jsx(CascadingMenuButton, { menuItems: [
-                                                {
-                                                    label: 'Download TSV',
-                                                    onClick: () => {
-                                                        saveAs(new Blob([resultsTsv || ''], {
-                                                            type: 'text/plain;charset=utf-8',
-                                                        }), 'scores.tsv');
-                                                    },
-                                                },
-                                                {
-                                                    label: showAdvanced
-                                                        ? 'Hide advanced options'
-                                                        : 'Show advanced options',
-                                                    onClick: () => {
-                                                        setShowAdvanced(!showAdvanced);
-                                                    },
-                                                },
-                                            ], children: _jsx(MenuIcon, {}) }) }), _jsx("div", { children: showAdvanced ? (_jsxs("div", { children: [_jsx(Typography, { variant: "h6", children: "Advanced options" }), _jsx(RadioGroup, { children: Object.entries({
-                                                        single: 'Single',
-                                                        complete: 'Complete',
-                                                    }).map(([key, val]) => (_jsx(FormControlLabel, { control: _jsx(Radio, { checked: clusterMethod === key, onChange: () => {
-                                                                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 => {
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [children, _jsxs("div", { style: { marginTop: 50 }, children: [_jsxs("div", { children: [_jsxs("div", { style: {
+                                            display: 'flex',
+                                            gap: '8px',
+                                            flexWrap: 'wrap',
+                                            marginBottom: '16px',
+                                        }, children: [_jsx(Button, { variant: "contained", onClick: () => {
+                                                    saveAs(new Blob([results || ''], {
+                                                        type: 'text/plain;charset=utf-8',
+                                                    }), 'cluster.R');
+                                                }, children: "Download Rscript" }), ' ', "or", ' ', _jsx(Button, { variant: "contained", onClick: () => {
+                                                    copy(results || '');
+                                                }, children: "Copy Rscript to clipboard" }), ' ', "or", ' ', _jsx(Button, { variant: "contained", onClick: () => {
+                                                    saveAs(new Blob([resultsTsv || ''], {
+                                                        type: 'text/plain;charset=utf-8',
+                                                    }), 'scores.tsv');
+                                                }, children: "Download TSV" })] }), _jsx("div", { children: _jsx(Button, { variant: "contained", onClick: () => {
+                                                setShowAdvanced(!showAdvanced);
+                                            }, children: showAdvanced
+                                                ? 'Hide advanced options'
+                                                : 'Show advanced options' }) }), showAdvanced ? (_jsxs("div", { children: [_jsx(Typography, { variant: "h6", children: "Advanced options" }), _jsx(RadioGroup, { children: Object.entries({
+                                                    single: 'Single',
+                                                    complete: 'Complete',
+                                                }).map(([key, val]) => (_jsx(FormControlLabel, { control: _jsx(Radio, { checked: clusterMethod === key, onChange: () => {
+                                                            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 => {
                                             setPaste(event.target.value);
                                         }, slotProps: {
                                             input: {
@@ -147,4 +137,4 @@ cat(resultClusters$order,sep='\\n')`
                             handleClose();
                         }, children: "Cancel" })] })] }));
 });
-export default ClusterDialogManuals;
+export default WiggleClusterDialogManuals;

package/esm/MultiLinearWiggleDisplay/components/YScaleBars.js

@@ -16,7 +16,7 @@ const Wrapper = observer(function ({ children, model, exportSVG, }) {
 });
 export const YScaleBars = observer(function (props) {
     const { model, orientation, exportSVG } = props;
-    const { stats, needsFullHeightScalebar, sources } = model;
-    return stats && sources ? (_jsx(Wrapper, { ...props, children: needsFullHeightScalebar ? (_jsx(FullHeightScaleBar, { model: model, orientation: orientation, exportSVG: exportSVG })) : (_jsx(IndividualScaleBars, { model: model, orientation: orientation, exportSVG: exportSVG })) })) : null;
+    const { showSidebar, stats, needsFullHeightScalebar, sources } = model;
+    return stats && sources ? (_jsx(Wrapper, { ...props, children: showSidebar ? (needsFullHeightScalebar ? (_jsx(FullHeightScaleBar, { model: model, orientation: orientation, exportSVG: exportSVG })) : (_jsx(IndividualScaleBars, { model: model, orientation: orientation, exportSVG: exportSVG }))) : null })) : null;
 });
 export default YScaleBars;

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

@@ -1,12 +1,13 @@
 import type { WiggleDisplayModel } from '../model';
+import type { GridRowId } from '@mui/x-data-grid';
 export declare function moveUp(arr: {
     name: string;
-}[], sel: string[], by?: number): {
+}[], sel: GridRowId[], by?: number): {
     name: string;
 }[];
 export declare function moveDown(arr: {
     name: string;
-}[], sel: string[], by?: number): {
+}[], sel: GridRowId[], by?: number): {
     name: string;
 }[];
 export declare function getOffset(model: WiggleDisplayModel): number;

package/esm/MultiLinearWiggleDisplay/model.d.ts

@@ -101,6 +101,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
 } & {
     type: import("mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
     layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
+    showSidebar: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -213,7 +214,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -327,6 +328,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     featureUnderMouseVolatile: Feature | undefined;
     sourcesVolatile: Source[] | undefined;
 } & {
+    setShowSidebar(arg: boolean): void;
     setSourcesLoading(str: string): void;
     setLayout(layout: Source[]): void;
     clearLayout(): void;

package/esm/MultiLinearWiggleDisplay/model.js

@@ -11,7 +11,7 @@ import { YSCALEBAR_LABEL_OFFSET, getScale } from '../util';
 const randomColor = () => '#000000'.replaceAll('0', () => (~~(Math.random() * 16)).toString(16));
 const Tooltip = lazy(() => import('./components/Tooltip'));
 const SetColorDialog = lazy(() => import('./components/SetColorDialog'));
-const ClusterDialog = lazy(() => import('./components/ClusterDialog/ClusterDialog'));
+const WiggleClusterDialog = lazy(() => import('./components/WiggleClusterDialog/WiggleClusterDialog'));
 const rendererTypes = new Map([
     ['xyplot', 'MultiXYPlotRenderer'],
     ['multirowxy', 'MultiRowXYPlotRenderer'],
@@ -24,6 +24,7 @@ export function stateModelFactory(_pluginManager, configSchema) {
         .compose('MultiLinearWiggleDisplay', SharedWiggleMixin(configSchema), types.model({
         type: types.literal('MultiLinearWiggleDisplay'),
         layout: types.optional(types.frozen(), []),
+        showSidebar: true,
     }))
         .volatile(() => ({
         sourcesLoadingStopToken: undefined,
@@ -31,6 +32,9 @@ export function stateModelFactory(_pluginManager, configSchema) {
         sourcesVolatile: undefined,
     }))
         .actions(self => ({
+        setShowSidebar(arg) {
+            self.showSidebar = arg;
+        },
         setSourcesLoading(str) {
             if (self.sourcesLoadingStopToken) {
                 stopStopToken(self.sourcesLoadingStopToken);
@@ -306,7 +310,7 @@ export function stateModelFactory(_pluginManager, configSchema) {
                         label: 'Cluster by score',
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
-                                ClusterDialog,
+                                WiggleClusterDialog,
                                 {
                                     model: self,
                                     handleClose,
@@ -314,6 +318,14 @@ export function stateModelFactory(_pluginManager, configSchema) {
                             ]);
                         },
                     },
+                    {
+                        label: 'Show sidebar',
+                        type: 'checkbox',
+                        checked: self.showSidebar,
+                        onClick: () => {
+                            self.setShowSidebar(!self.showSidebar);
+                        },
+                    },
                     {
                         label: 'Edit colors/arrangement...',
                         onClick: () => {

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

@@ -26,6 +26,5 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
         name: string;
         __name: unknown;
     }[]>;
-    freeResources(): void;
 }
 export {};

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -74,7 +74,6 @@ class MultiWiggleAdapter extends BaseFeatureDataAdapter {
             ...rest,
         }));
     }
-    freeResources() { }
 }
 MultiWiggleAdapter.capabilities = [
     'hasResolution',

package/esm/WiggleBaseRenderer.d.ts

@@ -33,7 +33,7 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        canvasRecordedData: any;
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -41,15 +41,15 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<string, Feature>;
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
         html?: string;
     }>;
     abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;

package/esm/WiggleBaseRenderer.js

@@ -26,7 +26,7 @@ export default class WiggleBaseRenderer extends FeatureRendererType {
             ...results,
             ...rest,
             features: reducedFeatures
-                ? new Map(reducedFeatures.map((r) => [r.id(), r]))
+                ? new Map(reducedFeatures.map(r => [r.id(), r]))
                 : results.features,
             height,
             width,

package/esm/WiggleRPC/MultiWiggleClusterScoreMatrix.js

@@ -1,5 +1,5 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { clusterData } from './cluster';
+import { clusterData } from '@jbrowse/core/util/cluster';
 import { getScoreMatrix } from './getScoreMatrix';
 export class MultiWiggleClusterScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
@@ -17,11 +17,8 @@ export class MultiWiggleClusterScoreMatrix extends RpcMethodTypeWithFiltersAndRe
             stopToken: deserializedArgs.stopToken,
             onProgress: a => {
                 var _a;
-                (_a = deserializedArgs.statusCallback) === null || _a === void 0 ? void 0 : _a.call(deserializedArgs, `${toP(a * 100)}%`);
+                (_a = deserializedArgs.statusCallback) === null || _a === void 0 ? void 0 : _a.call(deserializedArgs, a);
             },
         });
     }
 }
-function toP(n) {
-    return Number.parseFloat(n.toPrecision(3));
-}

package/esm/drawDensity.js

@@ -36,15 +36,21 @@ export function drawDensity(ctx, props) {
             start = performance.now();
         }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx) || rightPx - leftPx > 1) {
             reducedFeatures.push(feature);
             prevLeftPx = leftPx;
         }
         const score = feature.get('score');
         hasClipping = hasClipping || score > niceMax || score < niceMin;
         const w = rightPx - leftPx + fudgeFactor;
-        ctx.fillStyle = cb(feature, score);
-        ctx.fillRect(leftPx, 0, w, height);
+        if (score >= scaleOpts.domain[0]) {
+            ctx.fillStyle = cb(feature, score);
+            ctx.fillRect(leftPx, 0, w, height);
+        }
+        else {
+            ctx.fillStyle = '#eee';
+            ctx.fillRect(leftPx, 0, w, height);
+        }
     }
     ctx.save();
     if (hasClipping) {
@@ -66,5 +72,7 @@ export function drawDensity(ctx, props) {
         }
     }
     ctx.restore();
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/esm/drawLine.js

@@ -25,7 +25,7 @@ export function drawLine(ctx, props) {
             start = performance.now();
         }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx) || rightPx - leftPx > 1) {
             reducedFeatures.push(feature);
             prevLeftPx = leftPx;
         }
@@ -68,5 +68,7 @@ export function drawLine(ctx, props) {
             ctx.stroke();
         }
     }
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/esm/drawXY.js

@@ -89,7 +89,8 @@ export function drawXY(ctx, props) {
                         .toString())
                 : c;
             const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
-            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
+                rightPx - leftPx > 1) {
                 reducedFeatures.push(feature);
                 prevLeftPx = leftPx;
             }
@@ -128,7 +129,8 @@ export function drawXY(ctx, props) {
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
+                rightPx - leftPx > 1) {
                 reducedFeatures.push(feature);
                 prevLeftPx = leftPx;
             }
@@ -180,5 +182,7 @@ export function drawXY(ctx, props) {
             ctx.stroke();
         }
     }
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/esm/shared/SharedWiggleMixin.d.ts

@@ -206,7 +206,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "3.2.0",
+  "version": "3.4.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,14 +36,14 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bbi": "^6.0.0",
-    "@jbrowse/core": "^3.2.0",
-    "@jbrowse/plugin-data-management": "^3.2.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.2.0",
-    "@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",
+    "@gmod/bbi": "^7.0.0",
+    "@jbrowse/core": "^3.4.0",
+    "@jbrowse/plugin-data-management": "^3.4.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.4.0",
+    "@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": "c750e3f56706a490c19ba75abd807fec5e38aebf"
+  "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
 }

package/dist/WiggleRPC/cluster.d.ts

@@ -1,17 +0,0 @@
-export declare function euclideanDistance(a: number[], b: number[]): number;
-export declare function averageDistance(setA: number[], setB: number[], distances: number[][]): number;
-export declare function clusterData({ data, distance, linkage, onProgress, stopToken, }: {
-    data: number[][];
-    distance?: (a: number[], b: number[]) => number;
-    linkage?: (a: number[], b: number[], distances: number[][]) => number;
-    onProgress?: (a: number) => void;
-    stopToken?: string;
-}): {
-    clusters: {
-        height: number;
-        indexes: number[];
-    } | undefined;
-    distances: number[][];
-    order: number[];
-    clustersGivenK: number[][][];
-};

package/dist/WiggleRPC/cluster.js

@@ -1,84 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.euclideanDistance = euclideanDistance;
-exports.averageDistance = averageDistance;
-exports.clusterData = clusterData;
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-function euclideanDistance(a, b) {
-    const size = Math.min(a.length, b.length);
-    let sum = 0;
-    for (let index = 0; index < size; index++) {
-        sum += (a[index] - b[index]) * (a[index] - b[index]);
-    }
-    return Math.sqrt(sum);
-}
-function averageDistance(setA, setB, distances) {
-    let distance = 0;
-    for (const a of setA) {
-        for (const b of setB) {
-            distance += distances[a][b];
-        }
-    }
-    return distance / setA.length / setB.length;
-}
-function updateProgress(stepNumber, stepProgress, onProgress) {
-    onProgress(stepNumber / 2 + stepProgress / 2);
-}
-function clusterData({ data, distance = euclideanDistance, linkage = averageDistance, onProgress, stopToken, }) {
-    const distances = data.map((datum, index) => {
-        if (onProgress) {
-            updateProgress(0, index / (data.length - 1), onProgress);
-        }
-        return data.map(otherDatum => distance(datum, otherDatum));
-    });
-    const clusters = data.map((_datum, index) => ({
-        height: 0,
-        indexes: [Number(index)],
-    }));
-    let clustersGivenK = [];
-    let start = performance.now();
-    for (let iteration = 0; iteration < data.length; iteration++) {
-        if (performance.now() - start > 2000) {
-            (0, stopToken_1.checkStopToken)(stopToken);
-            start = performance.now();
-        }
-        if (onProgress) {
-            updateProgress(1, (iteration + 1) / data.length, onProgress);
-        }
-        clustersGivenK.push(clusters.map(cluster => cluster.indexes));
-        if (iteration >= data.length - 1) {
-            break;
-        }
-        let nearestDistance = Infinity;
-        let nearestRow = 0;
-        let nearestCol = 0;
-        for (let row = 0; row < clusters.length; row++) {
-            for (let col = row + 1; col < clusters.length; col++) {
-                const distance = linkage(clusters[row].indexes, clusters[col].indexes, distances);
-                if (distance < nearestDistance) {
-                    nearestDistance = distance;
-                    nearestRow = row;
-                    nearestCol = col;
-                }
-            }
-        }
-        const newCluster = {
-            indexes: [
-                ...clusters[nearestRow].indexes,
-                ...clusters[nearestCol].indexes,
-            ],
-            height: nearestDistance,
-            children: [clusters[nearestRow], clusters[nearestCol]],
-        };
-        clusters.splice(Math.max(nearestRow, nearestCol), 1);
-        clusters.splice(Math.min(nearestRow, nearestCol), 1);
-        clusters.push(newCluster);
-    }
-    clustersGivenK = [[], ...clustersGivenK.reverse()];
-    return {
-        clusters: clusters[0],
-        distances: distances,
-        order: clusters[0].indexes,
-        clustersGivenK: clustersGivenK,
-    };
-}