@jbrowse/plugin-variants 3.0.5 → 3.2.0

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,7 +1,7 @@
 import IntervalTree from '@flatten-js/interval-tree';
 import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip, getProgressDisplayStr } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import VcfFeature from '../VcfFeature';
@@ -45,7 +45,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
                 }
             }
             if (i++ % 10000 === 0) {
-                statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+                statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
             }
             blockStart = n + 1;
         }
@@ -96,9 +96,12 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             try {
                 const { start, end, refName } = region;
                 const { intervalTreeMap } = await this.setup();
-                (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
+                for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
+                    start,
+                    end,
+                ])) || []) {
                     observer.next(f);
-                });
+                }
                 observer.complete();
             }
             catch (e) {

package/esm/VcfAdapter/configSchema.js

@@ -16,5 +16,18 @@ const VcfAdapter = ConfigurationSchema('VcfAdapter', {
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                vcfLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 export default VcfAdapter;

package/esm/VcfFeature/util.js

@@ -17,7 +17,7 @@ export function getSOTermAndDescription(ref, alt, parser) {
     }
     const soTerms = new Set();
     let descriptions = new Set();
-    alt.forEach(a => {
+    for (const a of alt) {
         let [soTerm, description] = getSOAndDescFromAltDefs(a, parser);
         if (!soTerm) {
             ;
@@ -27,7 +27,7 @@ export function getSOTermAndDescription(ref, alt, parser) {
             soTerms.add(soTerm);
             descriptions.add(description);
         }
-    });
+    }
     if (descriptions.size > 1) {
         const descs = [...descriptions];
         const prefixes = new Set(descs

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -86,16 +86,21 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
             const header = lines[0].split('\t');
             const { parser } = await this.configure();
             const s = new Set(parser.samples);
-            return lines
+            const ret = lines
                 .slice(1)
+                .filter(f => !!f)
                 .map(line => {
-                const cols = line.split('\t');
+                const [name, ...rest] = line.split('\t');
                 return {
-                    name: cols[0],
-                    ...Object.fromEntries(cols.slice(1).map((c, idx) => [header[idx + 1], c])),
+                    ...Object.fromEntries(rest.map((c, idx) => [header[idx + 1], c])),
+                    name: name,
                 };
-            })
-                .filter(f => s.has(f.name));
+            });
+            const missing = ret.filter(f => !s.has(f.name));
+            if (missing.length) {
+                console.warn('Samples in metadata file not in VCF:', ret.filter(f => !s.has(f.name)));
+            }
+            return ret.filter(f => s.has(f.name));
         }
     }
     freeResources() { }

package/esm/VcfTabixAdapter/configSchema.js

@@ -4,7 +4,10 @@ function x() { }
 const VcfTabixAdapter = ConfigurationSchema('VcfTabixAdapter', {
     vcfGzLocation: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
+        defaultValue: {
+            uri: '/path/to/my.vcf.gz',
+            locationType: 'UriLocation',
+        },
     },
     index: ConfigurationSchema('VcfIndex', {
         indexType: {
@@ -28,5 +31,24 @@ const VcfTabixAdapter = ConfigurationSchema('VcfTabixAdapter', {
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                vcfGzLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                index: {
+                    location: {
+                        uri: `${snap.uri}.tbi`,
+                        baseUri: snap.baseUri,
+                    },
+                },
+            }
+            : snap;
+    },
+});
 export default VcfTabixAdapter;

package/esm/index.js

@@ -8,6 +8,7 @@ import MultiVariantRendererF from './MultiLinearVariantRenderer';
 import SplitVcfTabixAdapterF from './SplitVcfTabixAdapter';
 import StructuralVariantChordRendererF from './StructuralVariantChordRenderer';
 import VariantFeatureWidgetF from './VariantFeatureWidget';
+import { MultiVariantClusterGenotypeMatrix } from './VariantRPC/MultiVariantClusterGenotypeMatrix';
 import { MultiVariantGetGenotypeMatrix } from './VariantRPC/MultiVariantGetGenotypeMatrix';
 import { MultiVariantGetSimplifiedFeatures } from './VariantRPC/MultiVariantGetSimplifiedFeatures';
 import { MultiVariantGetSources } from './VariantRPC/MultiVariantGetSources';
@@ -36,6 +37,7 @@ export default class VariantsPlugin extends Plugin {
         ChordVariantDisplayF(pluginManager);
         pluginManager.addRpcMethod(() => new MultiVariantGetSources(pluginManager));
         pluginManager.addRpcMethod(() => new MultiVariantGetGenotypeMatrix(pluginManager));
+        pluginManager.addRpcMethod(() => new MultiVariantClusterGenotypeMatrix(pluginManager));
         pluginManager.addRpcMethod(() => new MultiVariantGetSimplifiedFeatures(pluginManager));
     }
 }

package/esm/shared/MultiVariantBaseModel.d.ts

@@ -255,6 +255,15 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     setSampleInfo(arg: Record<string, SampleInfo>): void;
 } & {
     readonly preSources: Source[] | undefined;
+    readonly sourcesWithoutLayout: {
+        label: string;
+        id: string;
+        baseUri?: string;
+        name: string;
+        color?: string;
+        group?: string;
+        HP?: number;
+    }[] | undefined;
     readonly sources: {
         label: string;
         id: string;
@@ -330,10 +339,20 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
         type?: undefined;
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        checked?: undefined;
+        subMenu?: undefined;
     })[];
 } & {
     readonly canDisplayLabels: boolean;
     readonly totalHeight: number;
+    readonly featuresReady: boolean;
 } & {
     renderProps(): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/shared/MultiVariantBaseModel.js

@@ -3,15 +3,17 @@ import { ConfigurationReference } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { stopStopToken } from '@jbrowse/core/util/stopToken';
 import { linearBareDisplayStateModelFactory } from '@jbrowse/plugin-linear-genome-view';
+import CategoryIcon from '@mui/icons-material/Category';
 import FilterListIcon from '@mui/icons-material/FilterList';
 import HeightIcon from '@mui/icons-material/Height';
 import SplitscreenIcon from '@mui/icons-material/Splitscreen';
 import VisibilityIcon from '@mui/icons-material/Visibility';
 import deepEqual from 'fast-deep-equal';
 import { types } from 'mobx-state-tree';
+import { getSources } from './getSources';
 const SetColorDialog = lazy(() => import('./components/SetColorDialog'));
 const MAFFilterDialog = lazy(() => import('./components/MAFFilterDialog'));
-const ClusterDialog = lazy(() => import('./components/ClusterDialog'));
+const ClusterDialog = lazy(() => import('./components/ClusterDialog/ClusterDialog'));
 const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog'));
 export default function MultiVariantBaseModelF(configSchema) {
     return types
@@ -86,40 +88,26 @@ export default function MultiVariantBaseModelF(configSchema) {
         get preSources() {
             return self.layout.length ? self.layout : self.sourcesVolatile;
         },
+        get sourcesWithoutLayout() {
+            return self.sourcesVolatile
+                ? getSources({
+                    sources: self.sourcesVolatile,
+                    renderingMode: self.renderingMode,
+                    sampleInfo: self.sampleInfo,
+                })
+                : undefined;
+        },
         get sources() {
-            var _a, _b;
-            if (this.preSources) {
-                const rows = [];
-                const sources = Object.fromEntries(((_a = self.sourcesVolatile) === null || _a === void 0 ? void 0 : _a.map(s => [s.name, s])) || []);
-                for (const row of this.preSources) {
-                    if (self.renderingMode === 'phased') {
-                        const info = (_b = self.sampleInfo) === null || _b === void 0 ? void 0 : _b[row.name];
-                        if (info === null || info === void 0 ? void 0 : info.isPhased) {
-                            const ploidy = info.maxPloidy;
-                            for (let i = 0; i < ploidy; i++) {
-                                const id = `${row.name} HP${i}`;
-                                rows.push({
-                                    ...sources[row.name],
-                                    ...row,
-                                    label: id,
-                                    HP: i,
-                                    id: id,
-                                });
-                            }
-                        }
-                    }
-                    else {
-                        rows.push({
-                            ...sources[row.name],
-                            ...row,
-                            label: row.name,
-                            id: row.name,
-                        });
-                    }
-                }
-                return rows;
-            }
-            return undefined;
+            const sourcesWithLayout = self.layout.length
+                ? self.layout
+                : self.sourcesVolatile;
+            return sourcesWithLayout
+                ? getSources({
+                    sources: sourcesWithLayout,
+                    renderingMode: self.renderingMode,
+                    sampleInfo: self.sampleInfo,
+                })
+                : undefined;
         },
     }))
         .views(self => {
@@ -222,6 +210,7 @@ export default function MultiVariantBaseModelF(configSchema) {
                     },
                     {
                         label: 'Cluster by genotype',
+                        icon: CategoryIcon,
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 ClusterDialog,
@@ -256,13 +245,16 @@ export default function MultiVariantBaseModelF(configSchema) {
             var _a;
             return self.rowHeight * (((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1);
         },
+        get featuresReady() {
+            return !!self.featuresVolatile;
+        },
     }))
         .views(self => ({
         renderProps() {
             const superProps = self.adapterProps();
             return {
                 ...superProps,
-                notReady: superProps.notReady || !self.sources || !self.featuresVolatile,
+                notReady: superProps.notReady || !self.sources || !self.featuresReady,
                 height: self.height,
                 totalHeight: self.totalHeight,
                 renderingMode: self.renderingMode,

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

@@ -0,0 +1,6 @@
+import type { ReducedModel } from './types';
+declare const ClusterDialog: ({ model, handleClose, }: {
+    model: ReducedModel;
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ClusterDialog;

package/esm/shared/components/ClusterDialog/ClusterDialog.js

@@ -0,0 +1,24 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { FormControlLabel, Radio, RadioGroup, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import ClusterDialogAuto from './ClusterDialogAuto';
+import ClusterDialogManual from './ClusterDialogManual';
+function Header({ activeMode, setActiveMode, }) {
+    return (_jsxs("div", { children: [_jsx(Typography, { style: { marginBottom: 30 }, children: "This procedure will cluster the visible genotype data using hierarchical clustering" }), _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)" })),
+                }).map(([key, val]) => (_jsx(FormControlLabel, { control: _jsx(Radio, { checked: activeMode === key, onChange: () => {
+                            setActiveMode(key);
+                        } }), label: val }, key))) })] }));
+}
+const ClusterDialog = observer(function ({ model, handleClose, }) {
+    const [activeMode, setActiveMode] = useState('auto');
+    return (_jsx(Dialog, { open: true, title: "Cluster by genotype", 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 }) })) }));
+});
+export default ClusterDialog;

package/esm/shared/components/ClusterDialog/ClusterDialogAuto.d.ts

@@ -0,0 +1,7 @@
+import type { ReducedModel } from './types';
+declare const ClusterDialogAuto: ({ model, children, handleClose, }: {
+    model: ReducedModel;
+    children: React.ReactNode;
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ClusterDialogAuto;

package/esm/shared/components/ClusterDialog/ClusterDialogAuto.js

@@ -0,0 +1,67 @@
+import { jsxs as _jsxs, jsx as _jsx, Fragment as _Fragment } from "react/jsx-runtime";
+import { useState } from 'react';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { getContainingView, getSession, isAbortException, } from '@jbrowse/core/util';
+import { createStopToken, stopStopToken } from '@jbrowse/core/util/stopToken';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { Button, DialogActions, DialogContent } from '@mui/material';
+import { observer } from 'mobx-react';
+import { isAlive } from 'mobx-state-tree';
+const ClusterDialogAuto = observer(function ({ model, children, handleClose, }) {
+    const [progress, setProgress] = useState('');
+    const [error, setError] = useState();
+    const [stopToken, setStopToken] = useState('');
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [children, _jsxs("div", { children: [progress ? (_jsxs("div", { style: { padding: 50 }, children: [_jsxs("span", { style: { width: 400 }, children: ["Progress: ", progress] }), _jsx(Button, { onClick: () => {
+                                            stopStopToken(stopToken);
+                                        }, children: "Stop" })] })) : null, error ? _jsx(ErrorMessage, { error: error }) : null] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", onClick: async () => {
+                            try {
+                                setError(undefined);
+                                const view = getContainingView(model);
+                                if (!view.initialized) {
+                                    return;
+                                }
+                                const { rpcManager } = getSession(model);
+                                const { sourcesWithoutLayout, minorAlleleFrequencyFilter, adapterConfig, } = model;
+                                if (sourcesWithoutLayout) {
+                                    const sessionId = getRpcSessionId(model);
+                                    const stopToken = createStopToken();
+                                    setStopToken(stopToken);
+                                    const ret = (await rpcManager.call(sessionId, 'MultiVariantClusterGenotypeMatrix', {
+                                        regions: view.dynamicBlocks.contentBlocks,
+                                        sources: sourcesWithoutLayout,
+                                        minorAlleleFrequencyFilter,
+                                        sessionId,
+                                        adapterConfig,
+                                        stopToken,
+                                        statusCallback: (arg) => {
+                                            setProgress(arg);
+                                        },
+                                    }));
+                                    model.setLayout(ret.order.map(idx => {
+                                        const ret = sourcesWithoutLayout[idx];
+                                        if (!ret) {
+                                            throw new Error(`out of bounds at ${idx}`);
+                                        }
+                                        return ret;
+                                    }));
+                                }
+                                handleClose();
+                            }
+                            catch (e) {
+                                if (!isAbortException(e) && isAlive(model)) {
+                                    console.error(e);
+                                    setError(e);
+                                }
+                            }
+                            finally {
+                                setProgress('');
+                                setStopToken('');
+                            }
+                        }, children: "Run clustering" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                            if (stopToken) {
+                                stopStopToken(stopToken);
+                            }
+                        }, children: "Cancel" })] })] }));
+});
+export default ClusterDialogAuto;

package/esm/shared/components/ClusterDialog/ClusterDialogManual.d.ts

@@ -0,0 +1,7 @@
+import type { ReducedModel } from './types';
+declare const ClusterDialogManuals: ({ model, handleClose, children, }: {
+    model: ReducedModel;
+    handleClose: () => void;
+    children: React.ReactNode;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ClusterDialogManuals;

package/esm/shared/components/ClusterDialog/ClusterDialogManual.js

@@ -0,0 +1,139 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { getContainingView, getSession, isAbortException, useLocalStorage, } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { Button, DialogActions, DialogContent, FormControlLabel, Paper, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
+import copy from 'copy-to-clipboard';
+import { saveAs } from 'file-saver';
+import { observer } from 'mobx-react';
+import { isAlive } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+    mgap: {
+        display: 'flex',
+        flexDirection: 'column',
+        gap: theme.spacing(4),
+    },
+}));
+const ClusterDialogManuals = 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');
+    useEffect(() => {
+        ;
+        (async () => {
+            try {
+                setError(undefined);
+                setRet(undefined);
+                setLoading(true);
+                const view = getContainingView(model);
+                if (!view.initialized) {
+                    return;
+                }
+                const { rpcManager } = getSession(model);
+                const { sourcesWithoutLayout, minorAlleleFrequencyFilter, adapterConfig, } = model;
+                const sessionId = getRpcSessionId(model);
+                const ret = (await rpcManager.call(sessionId, 'MultiVariantGetGenotypeMatrix', {
+                    regions: view.dynamicBlocks.contentBlocks,
+                    sources: sourcesWithoutLayout,
+                    minorAlleleFrequencyFilter,
+                    sessionId,
+                    adapterConfig,
+                }));
+                setRet(ret);
+            }
+            catch (e) {
+                if (!isAbortException(e) && isAlive(model)) {
+                    console.error(e);
+                    setError(e);
+                }
+            }
+            finally {
+                setLoading(false);
+            }
+        })();
+    }, [model]);
+    const results = ret
+        ? `inputMatrix<-matrix(c(${Object.values(ret)
+            .map(val => val.join(','))
+            .join(',\n')}
+),nrow=${Object.values(ret).length},byrow=TRUE)
+rownames(inputMatrix)<-c(${Object.keys(ret)
+            .map(key => `'${key}'`)
+            .join(',')})
+resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
+cat(resultClusters$order,sep='\\n')`
+        : undefined;
+    const resultsTsv = ret
+        ? Object.entries(ret)
+            .map(([key, val]) => [key, ...val].join('\t'))
+            .join('\n')
+        : undefined;
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [children, _jsxs(Paper, { style: { padding: 16 }, 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',
+                                            }), 'genotypes.tsv');
+                                        }, children: "Download TSV" }), _jsxs("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))) })] })) : null] }), results ? (_jsx("div", {})) : loading ? (_jsx(LoadingEllipses, { variant: "h6", title: "Generating genotype 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: {
+                                                classes: {
+                                                    input: classes.textAreaFont,
+                                                },
+                                            },
+                                        } })] })] })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", onClick: () => {
+                            const { sourcesWithoutLayout } = model;
+                            if (sourcesWithoutLayout) {
+                                try {
+                                    model.setLayout(paste
+                                        .split('\n')
+                                        .map(t => t.trim())
+                                        .filter(f => !!f)
+                                        .map(r => +r)
+                                        .map(idx => {
+                                        const ret = sourcesWithoutLayout[idx - 1];
+                                        if (!ret) {
+                                            throw new Error(`out of bounds at ${idx}`);
+                                        }
+                                        return ret;
+                                    }));
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    getSession(model).notifyError(`${e}`, e);
+                                }
+                            }
+                            handleClose();
+                        }, children: "Apply clustering" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
+});
+export default ClusterDialogManuals;

package/esm/shared/components/ClusterDialog/types.d.ts

@@ -0,0 +1,9 @@
+import type { Source } from '../../types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export interface ReducedModel {
+    sourcesWithoutLayout?: Source[];
+    minorAlleleFrequencyFilter?: number;
+    adapterConfig: AnyConfigurationModel;
+    setLayout: (arg: Source[]) => void;
+    clearLayout: () => void;
+}

package/esm/shared/components/ClusterDialog/types.js

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