@jbrowse/plugin-wiggle 3.2.0 → 3.4.0

package/dist/BigWigAdapter/BigWigAdapter.d.ts

@@ -21,6 +21,5 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
-    freeResources(): void;
 }
 export {};

package/dist/BigWigAdapter/BigWigAdapter.js

@@ -72,7 +72,6 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             featureDensity: 0,
         };
     }
-    freeResources() { }
 }
 BigWigAdapter.capabilities = [
     'hasResolution',

package/dist/LinearWiggleDisplay/model.d.ts

@@ -212,7 +212,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/dist/MultiLinearWiggleDisplay/components/SourcesGrid.js

@@ -87,8 +87,8 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                     onChange([...rows]);
                 }, onClose: () => {
                     setAnchorEl(null);
-                } }), (0, jsx_runtime_1.jsx)("div", { style: { height: 400, width: '100%' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { getRowId: row => row.name, checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
-                        setSelected(arg);
+                } }), (0, jsx_runtime_1.jsx)("div", { style: { height: 400, width: '100%' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { getRowId: row => row.name, checkboxSelection: true, onRowSelectionModelChange: arg => {
+                        setSelected([...arg.ids]);
                     }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
                         {
                             field: 'color',

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

@@ -1,6 +1,6 @@
 import type { ReducedModel } from './types';
-declare const ClusterDialog: ({ model, handleClose, }: {
+declare const WiggleClusterDialog: ({ model, handleClose, }: {
     model: ReducedModel;
     handleClose: () => void;
 }) => import("react/jsx-runtime").JSX.Element;
-export default ClusterDialog;
+export default WiggleClusterDialog;

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

@@ -8,22 +8,22 @@ const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-const ClusterDialogAuto_1 = __importDefault(require("./ClusterDialogAuto"));
-const ClusterDialogManual_1 = __importDefault(require("./ClusterDialogManual"));
+const WiggleClusterDialogAuto_1 = __importDefault(require("./WiggleClusterDialogAuto"));
+const WiggleClusterDialogManual_1 = __importDefault(require("./WiggleClusterDialogManual"));
 function Header({ activeMode, setActiveMode, }) {
     return ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { children: Object.entries({
-                auto: ((0, jsx_runtime_1.jsx)("div", { children: "Run in-app clustering (slow for large data, built in JS clustering)" })),
-                manual: ((0, jsx_runtime_1.jsx)("div", { children: "Download R script to run clustering (faster for large data, uses hclust, may be more accurate)" })),
+                auto: ((0, jsx_runtime_1.jsx)("div", { children: "Run in-app clustering (slower, particularly for large numbers of samples, uses JS implementation of hclust)" })),
+                manual: ((0, jsx_runtime_1.jsx)("div", { children: "Download R script to run clustering (faster, uses R implementation of hclust)" })),
             }).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Radio, { checked: activeMode === key, onChange: () => {
                         setActiveMode(key);
                     } }), label: val }, key))) }) }));
 }
-const ClusterDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
+const WiggleClusterDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
     const [activeMode, setActiveMode] = (0, react_1.useState)('auto');
     return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, title: "Cluster by score", maxWidth: "xl", onClose: (_, reason) => {
             if (reason !== 'backdropClick') {
                 handleClose();
             }
-        }, children: activeMode === 'auto' ? ((0, jsx_runtime_1.jsx)(ClusterDialogAuto_1.default, { model: model, handleClose: handleClose, children: (0, jsx_runtime_1.jsx)(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) : ((0, jsx_runtime_1.jsx)(ClusterDialogManual_1.default, { model: model, handleClose: handleClose, children: (0, jsx_runtime_1.jsx)(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) }));
+        }, children: activeMode === 'auto' ? ((0, jsx_runtime_1.jsx)(WiggleClusterDialogAuto_1.default, { model: model, handleClose: handleClose, children: (0, jsx_runtime_1.jsx)(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) : ((0, jsx_runtime_1.jsx)(WiggleClusterDialogManual_1.default, { model: model, handleClose: handleClose, children: (0, jsx_runtime_1.jsx)(Header, { activeMode: activeMode, setActiveMode: setActiveMode }) })) }));
 });
-exports.default = ClusterDialog;
+exports.default = WiggleClusterDialog;

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

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

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

@@ -9,9 +9,10 @@ const tracks_1 = require("@jbrowse/core/util/tracks");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
-const ClusterDialogAuto = (0, mobx_react_1.observer)(function ({ model, children, handleClose, }) {
+const WiggleClusterDialogAuto = (0, mobx_react_1.observer)(function ({ model, children, handleClose, }) {
     const [progress, setProgress] = (0, react_1.useState)('');
     const [error, setError] = (0, react_1.useState)();
+    const [loading, setLoading] = (0, react_1.useState)(false);
     const [stopToken, setStopToken] = (0, react_1.useState)('');
     const [showAdvanced, setShowAdvanced] = (0, react_1.useState)(false);
     const [samplesPerPixel, setSamplesPerPixel] = (0, util_1.useLocalStorage)('cluster-samplesPerPixel', '1');
@@ -19,12 +20,13 @@ const ClusterDialogAuto = (0, mobx_react_1.observer)(function ({ model, children
                                     setShowAdvanced(!showAdvanced);
                                 }, children: showAdvanced ? 'Hide advanced options' : 'Show advanced options' }), showAdvanced ? ((0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 20 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This procedure samples the data at each 'pixel' across the visible by default" }), (0, jsx_runtime_1.jsx)(material_1.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] }), (0, jsx_runtime_1.jsxs)("div", { children: [progress ? ((0, jsx_runtime_1.jsxs)("div", { style: { padding: 50 }, children: [(0, jsx_runtime_1.jsxs)("span", { style: { width: 400 }, children: ["Progress: ", progress] }), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
+                                        } })] })) : null] }), (0, jsx_runtime_1.jsxs)("div", { children: [loading ? ((0, jsx_runtime_1.jsxs)("div", { style: { padding: 50 }, children: [(0, jsx_runtime_1.jsx)("span", { children: progress || 'Loading...' }), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
                                             (0, stopToken_1.stopStopToken)(stopToken);
-                                        }, children: "Stop" })] })) : null, 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, { variant: "contained", onClick: async () => {
+                                        }, children: "Stop" })] })) : null, 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, { variant: "contained", disabled: loading, onClick: async () => {
                             try {
                                 setError(undefined);
-                                setProgress('');
+                                setProgress('Initializing');
+                                setLoading(true);
                                 const view = (0, util_1.getContainingView)(model);
                                 if (!view.initialized) {
                                     return;
@@ -63,6 +65,7 @@ const ClusterDialogAuto = (0, mobx_react_1.observer)(function ({ model, children
                                 }
                             }
                             finally {
+                                setLoading(false);
                                 setProgress('');
                                 setStopToken('');
                             }
@@ -73,4 +76,4 @@ const ClusterDialogAuto = (0, mobx_react_1.observer)(function ({ model, children
                             }
                         }, children: "Cancel" })] })] }));
 });
-exports.default = ClusterDialogAuto;
+exports.default = WiggleClusterDialogAuto;

package/dist/MultiLinearWiggleDisplay/components/{ClusterDialog/ClusterDialogAuto.d.ts → WiggleClusterDialog/WiggleClusterDialogManual.d.ts}

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

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

@@ -8,7 +8,6 @@ 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 Menu_1 = __importDefault(require("@mui/icons-material/Menu"));
 const material_1 = require("@mui/material");
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const file_saver_1 = require("file-saver");
@@ -25,15 +24,15 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         gap: theme.spacing(4),
     },
 }));
-const ClusterDialogManuals = (0, mobx_react_1.observer)(function ({ model, handleClose, children, }) {
+const WiggleClusterDialogManuals = (0, mobx_react_1.observer)(function ({ model, handleClose, children, }) {
     const { classes } = useStyles();
     const [paste, setPaste] = (0, react_1.useState)('');
     const [ret, setRet] = (0, react_1.useState)();
     const [error, setError] = (0, react_1.useState)();
     const [loading, setLoading] = (0, react_1.useState)(false);
-    const [showAdvanced, setShowAdvanced] = (0, react_1.useState)(false);
-    const [clusterMethod, setClusterMethod] = (0, util_1.useLocalStorage)('cluster-clusterMethod', 'single');
-    const [samplesPerPixel, setSamplesPerPixel] = (0, util_1.useLocalStorage)('cluster-samplesPerPixel', '1');
+    const [showAdvanced, setShowAdvanced] = (0, util_1.useLocalStorage)('cluster-showAdvanced', false);
+    const [clusterMethod, setClusterMethod] = (0, react_1.useState)('single');
+    const [samplesPerPixel, setSamplesPerPixel] = (0, react_1.useState)('1');
     (0, react_1.useEffect)(() => {
         ;
         (async () => {
@@ -82,42 +81,33 @@ cat(resultClusters$order,sep='\\n')`
             .map(([key, val]) => [key, ...val].join('\t'))
             .join('\n')
         : undefined;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [children, (0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 50 }, children: [(0, jsx_runtime_1.jsxs)("div", { style: {
-                                    display: 'flex',
-                                    gap: '8px',
-                                    flexWrap: 'wrap',
-                                    marginBottom: '16px',
-                                }, children: [(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)("div", { style: { float: 'right' }, children: (0, jsx_runtime_1.jsx)(ui_1.CascadingMenuButton, { menuItems: [
-                                                {
-                                                    label: 'Download TSV',
-                                                    onClick: () => {
-                                                        (0, file_saver_1.saveAs)(new Blob([resultsTsv || ''], {
-                                                            type: 'text/plain;charset=utf-8',
-                                                        }), 'scores.tsv');
-                                                    },
-                                                },
-                                                {
-                                                    label: showAdvanced
-                                                        ? 'Hide advanced options'
-                                                        : 'Show advanced options',
-                                                    onClick: () => {
-                                                        setShowAdvanced(!showAdvanced);
-                                                    },
-                                                },
-                                            ], children: (0, jsx_runtime_1.jsx)(Menu_1.default, {}) }) }), (0, jsx_runtime_1.jsx)("div", { children: showAdvanced ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "h6", children: "Advanced options" }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { children: Object.entries({
-                                                        single: 'Single',
-                                                        complete: 'Complete',
-                                                    }).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Radio, { checked: clusterMethod === key, onChange: () => {
-                                                                setClusterMethod(key);
-                                                            } }), label: val }, key))) }), (0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 20 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This procedure samples the data at each 'pixel' across the visible by default" }), (0, jsx_runtime_1.jsx)(material_1.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 ? ((0, jsx_runtime_1.jsx)("div", {})) : loading ? ((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)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "subtitle2", gutterBottom: true, style: { marginTop: '16px' }, children: "Clustering Results:" }), (0, jsx_runtime_1.jsx)(material_1.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 ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [children, (0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 50 }, children: [(0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: {
+                                            display: 'flex',
+                                            gap: '8px',
+                                            flexWrap: 'wrap',
+                                            marginBottom: '16px',
+                                        }, children: [(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" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                                    (0, file_saver_1.saveAs)(new Blob([resultsTsv || ''], {
+                                                        type: 'text/plain;charset=utf-8',
+                                                    }), 'scores.tsv');
+                                                }, children: "Download TSV" })] }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                                setShowAdvanced(!showAdvanced);
+                                            }, children: showAdvanced
+                                                ? 'Hide advanced options'
+                                                : 'Show advanced options' }) }), showAdvanced ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "h6", children: "Advanced options" }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { children: Object.entries({
+                                                    single: 'Single',
+                                                    complete: 'Complete',
+                                                }).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Radio, { checked: clusterMethod === key, onChange: () => {
+                                                            setClusterMethod(key);
+                                                        } }), label: val }, key))) }), (0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 20 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This procedure samples the data at each 'pixel' across the visible by default" }), (0, jsx_runtime_1.jsx)(material_1.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 ? ((0, jsx_runtime_1.jsx)("div", {})) : loading ? ((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)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "subtitle2", gutterBottom: true, style: { marginTop: '16px' }, children: "Clustering Results:" }), (0, jsx_runtime_1.jsx)(material_1.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: {
@@ -152,4 +142,4 @@ cat(resultClusters$order,sep='\\n')`
                             handleClose();
                         }, children: "Cancel" })] })] }));
 });
-exports.default = ClusterDialogManuals;
+exports.default = WiggleClusterDialogManuals;

package/dist/MultiLinearWiggleDisplay/components/YScaleBars.js

@@ -22,7 +22,7 @@ const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSV
 });
 exports.YScaleBars = (0, mobx_react_1.observer)(function (props) {
     const { model, orientation, exportSVG } = props;
-    const { stats, needsFullHeightScalebar, sources } = model;
-    return stats && sources ? ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, children: needsFullHeightScalebar ? ((0, jsx_runtime_1.jsx)(FullHeightScaleBar_1.default, { model: model, orientation: orientation, exportSVG: exportSVG })) : ((0, jsx_runtime_1.jsx)(IndividualScaleBars_1.default, { model: model, orientation: orientation, exportSVG: exportSVG })) })) : null;
+    const { showSidebar, stats, needsFullHeightScalebar, sources } = model;
+    return stats && sources ? ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, children: showSidebar ? (needsFullHeightScalebar ? ((0, jsx_runtime_1.jsx)(FullHeightScaleBar_1.default, { model: model, orientation: orientation, exportSVG: exportSVG })) : ((0, jsx_runtime_1.jsx)(IndividualScaleBars_1.default, { model: model, orientation: orientation, exportSVG: exportSVG }))) : null })) : null;
 });
 exports.default = exports.YScaleBars;

package/dist/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/dist/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/dist/MultiLinearWiggleDisplay/model.js

@@ -50,7 +50,7 @@ const util_2 = require("../util");
 const randomColor = () => '#000000'.replaceAll('0', () => (~~(Math.random() * 16)).toString(16));
 const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Tooltip'))));
 const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetColorDialog'))));
-const ClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ClusterDialog/ClusterDialog'))));
+const WiggleClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/WiggleClusterDialog/WiggleClusterDialog'))));
 const rendererTypes = new Map([
     ['xyplot', 'MultiXYPlotRenderer'],
     ['multirowxy', 'MultiRowXYPlotRenderer'],
@@ -63,6 +63,7 @@ function stateModelFactory(_pluginManager, configSchema) {
         .compose('MultiLinearWiggleDisplay', (0, SharedWiggleMixin_1.default)(configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('MultiLinearWiggleDisplay'),
         layout: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
+        showSidebar: true,
     }))
         .volatile(() => ({
         sourcesLoadingStopToken: undefined,
@@ -70,6 +71,9 @@ function stateModelFactory(_pluginManager, configSchema) {
         sourcesVolatile: undefined,
     }))
         .actions(self => ({
+        setShowSidebar(arg) {
+            self.showSidebar = arg;
+        },
         setSourcesLoading(str) {
             if (self.sourcesLoadingStopToken) {
                 (0, stopToken_1.stopStopToken)(self.sourcesLoadingStopToken);
@@ -345,7 +349,7 @@ function stateModelFactory(_pluginManager, configSchema) {
                         label: 'Cluster by score',
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                ClusterDialog,
+                                WiggleClusterDialog,
                                 {
                                     model: self,
                                     handleClose,
@@ -353,6 +357,14 @@ function stateModelFactory(_pluginManager, configSchema) {
                             ]);
                         },
                     },
+                    {
+                        label: 'Show sidebar',
+                        type: 'checkbox',
+                        checked: self.showSidebar,
+                        onClick: () => {
+                            self.setShowSidebar(!self.showSidebar);
+                        },
+                    },
                     {
                         label: 'Edit colors/arrangement...',
                         onClick: () => {

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

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

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -76,7 +76,6 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             ...rest,
         }));
     }
-    freeResources() { }
 }
 MultiWiggleAdapter.capabilities = [
     'hasResolution',

package/dist/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/dist/WiggleBaseRenderer.js

@@ -31,7 +31,7 @@ class WiggleBaseRenderer extends FeatureRendererType_1.default {
             ...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/dist/WiggleRPC/MultiWiggleClusterScoreMatrix.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultiWiggleClusterScoreMatrix = void 0;
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
-const cluster_1 = require("./cluster");
+const cluster_1 = require("@jbrowse/core/util/cluster");
 const getScoreMatrix_1 = require("./getScoreMatrix");
 class MultiWiggleClusterScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
     constructor() {
@@ -23,12 +23,9 @@ class MultiWiggleClusterScoreMatrix extends RpcMethodTypeWithFiltersAndRenameReg
             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);
             },
         });
     }
 }
 exports.MultiWiggleClusterScoreMatrix = MultiWiggleClusterScoreMatrix;
-function toP(n) {
-    return Number.parseFloat(n.toPrecision(3));
-}

package/dist/drawDensity.js

@@ -39,15 +39,21 @@ function drawDensity(ctx, props) {
             start = performance.now();
         }
         const [leftPx, rightPx] = (0, util_1.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) {
@@ -69,5 +75,7 @@ function drawDensity(ctx, props) {
         }
     }
     ctx.restore();
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/dist/drawLine.js

@@ -28,7 +28,7 @@ function drawLine(ctx, props) {
             start = performance.now();
         }
         const [leftPx, rightPx] = (0, util_1.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;
         }
@@ -71,5 +71,7 @@ function drawLine(ctx, props) {
             ctx.stroke();
         }
     }
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/dist/drawXY.js

@@ -92,7 +92,8 @@ 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;
             }
@@ -131,7 +132,8 @@ function drawXY(ctx, props) {
                 start = performance.now();
             }
             const [leftPx, rightPx] = (0, util_1.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;
             }
@@ -183,5 +185,7 @@ function drawXY(ctx, props) {
             ctx.stroke();
         }
     }
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/dist/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/esm/BigWigAdapter/BigWigAdapter.d.ts

@@ -21,6 +21,5 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
-    freeResources(): void;
 }
 export {};

package/esm/BigWigAdapter/BigWigAdapter.js

@@ -70,7 +70,6 @@ class BigWigAdapter extends BaseFeatureDataAdapter {
             featureDensity: 0,
         };
     }
-    freeResources() { }
 }
 BigWigAdapter.capabilities = [
     'hasResolution',

package/esm/LinearWiggleDisplay/model.d.ts

@@ -212,7 +212,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.js

@@ -49,8 +49,8 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                     onChange([...rows]);
                 }, onClose: () => {
                     setAnchorEl(null);
-                } }), _jsx("div", { style: { height: 400, width: '100%' }, children: _jsx(DataGrid, { getRowId: row => row.name, checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
-                        setSelected(arg);
+                } }), _jsx("div", { style: { height: 400, width: '100%' }, children: _jsx(DataGrid, { getRowId: row => row.name, checkboxSelection: true, onRowSelectionModelChange: arg => {
+                        setSelected([...arg.ids]);
                     }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
                         {
                             field: 'color',

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

@@ -1,6 +1,6 @@
 import type { ReducedModel } from './types';
-declare const ClusterDialog: ({ model, handleClose, }: {
+declare const WiggleClusterDialog: ({ model, handleClose, }: {
     model: ReducedModel;
     handleClose: () => void;
 }) => import("react/jsx-runtime").JSX.Element;
-export default ClusterDialog;
+export default WiggleClusterDialog;