@jbrowse/plugin-linear-comparative-view 2.6.1

package/esm/LinearSyntenyView/components/ImportCustomTrack.js

@@ -0,0 +1,152 @@
+import React, { useState, useEffect } from 'react';
+import path from 'path';
+import { FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
+import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+function getName(sessionTrackData) {
+    return sessionTrackData
+        ? // @ts-expect-error
+            sessionTrackData.uri ||
+                // @ts-expect-error
+                sessionTrackData.localPath ||
+                // @ts-expect-error
+                sessionTrackData.name
+        : undefined;
+}
+function stripGz(fileName) {
+    return fileName.endsWith('.gz') ? fileName.slice(0, -3) : fileName;
+}
+function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Location, bed2Location, }) {
+    if (radioOption === '.paf') {
+        return {
+            type: 'PAFAdapter',
+            pafLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.out') {
+        return {
+            type: 'MashMapAdapter',
+            outLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.delta') {
+        return {
+            type: 'DeltaAdapter',
+            deltaLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.chain') {
+        return {
+            type: 'ChainAdapter',
+            chainLocation: fileLocation,
+            queryAssembly: assembly1,
+            targetAssembly: assembly2,
+        };
+    }
+    else if (radioOption === '.anchors') {
+        return {
+            type: 'MCScanAnchorsAdapter',
+            mcscanAnchorsLocation: fileLocation,
+            bed1Location,
+            bed2Location,
+            assemblyNames: [assembly1, assembly2],
+        };
+    }
+    else if (radioOption === '.anchors.simple') {
+        return {
+            type: 'MCScanSimpleAnchorsAdapter',
+            mcscanSimpleAnchorsLocation: fileLocation,
+            bed1Location,
+            bed2Location,
+            assemblyNames: [assembly1, assembly2],
+        };
+    }
+    else {
+        throw new Error('Unknown type');
+    }
+}
+const OpenTrack = observer(({ sessionTrackData, assembly1, assembly2, setSessionTrackData, }) => {
+    const [bed2Location, setBed2Location] = useState();
+    const [bed1Location, setBed1Location] = useState();
+    const [fileLocation, setFileLocation] = useState();
+    const [value, setValue] = useState('');
+    const [error, setError] = useState();
+    const fileName = getName(fileLocation);
+    const radioOption = value || (fileName ? path.extname(stripGz(fileName)) : '');
+    useEffect(() => {
+        try {
+            if (fileLocation) {
+                const fn = fileName ? path.basename(fileName) : 'MyTrack';
+                const trackId = `${fn}-${Date.now()}`;
+                setError(undefined);
+                setSessionTrackData({
+                    trackId,
+                    name: fn,
+                    assemblyNames: [assembly2, assembly1],
+                    type: 'SyntenyTrack',
+                    adapter: getAdapter({
+                        radioOption,
+                        assembly1,
+                        assembly2,
+                        fileLocation,
+                        bed1Location,
+                        bed2Location,
+                    }),
+                });
+            }
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }, [
+        fileName,
+        assembly1,
+        assembly2,
+        bed1Location,
+        bed2Location,
+        fileLocation,
+        radioOption,
+        setSessionTrackData,
+    ]);
+    return (React.createElement(Paper, { style: { padding: 12 } },
+        error ? React.createElement(ErrorMessage, { error: error }) : null,
+        React.createElement(Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view in the dotplot. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
+        React.createElement(RadioGroup, { value: radioOption, onChange: event => setValue(event.target.value) },
+            React.createElement(Grid, { container: true, justifyContent: "center" },
+                React.createElement(Grid, { item: true },
+                    React.createElement(FormControlLabel, { value: ".paf", control: React.createElement(Radio, null), label: ".paf" })),
+                React.createElement(Grid, { item: true },
+                    React.createElement(FormControlLabel, { value: ".out", control: React.createElement(Radio, null), label: ".out" })),
+                React.createElement(Grid, { item: true },
+                    React.createElement(FormControlLabel, { value: ".delta", control: React.createElement(Radio, null), label: ".delta" })),
+                React.createElement(Grid, { item: true },
+                    React.createElement(FormControlLabel, { value: ".chain", control: React.createElement(Radio, null), label: ".chain" })),
+                React.createElement(Grid, { item: true },
+                    React.createElement(FormControlLabel, { value: ".anchors", control: React.createElement(Radio, null), label: ".anchors" })),
+                React.createElement(Grid, { item: true },
+                    React.createElement(FormControlLabel, { value: ".anchors.simple", control: React.createElement(Radio, null), label: ".anchors.simple" })))),
+        React.createElement(Grid, { container: true, justifyContent: "center" },
+            React.createElement(Grid, { item: true }, value === '.anchors' || value === '.anchors.simple' ? (React.createElement("div", null,
+                React.createElement("div", { style: { margin: 20 } },
+                    "Open the ",
+                    value,
+                    " and .bed files for both genome assemblies from the MCScan (Python version) pipeline",
+                    ' ',
+                    React.createElement("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)" }, "(more info)")),
+                React.createElement("div", { style: { display: 'flex' } },
+                    React.createElement("div", null,
+                        React.createElement(FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) })),
+                    React.createElement("div", null,
+                        React.createElement(FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => setBed1Location(loc) })),
+                    React.createElement("div", null,
+                        React.createElement(FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => setBed2Location(loc) }))))) : (React.createElement(FileSelector, { name: value ? value + ' location' : '', description: "", location: fileLocation, setLocation: loc => setFileLocation(loc) }))))));
+});
+export default OpenTrack;
+//# sourceMappingURL=ImportCustomTrack.js.map

package/esm/LinearSyntenyView/components/ImportCustomTrack.js.map

@@ -0,0 +1 @@
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package/esm/LinearSyntenyView/components/ImportForm.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { LinearSyntenyViewModel } from '../model';
+declare const _default: ({ model, }: {
+    model: LinearSyntenyViewModel;
+}) => React.JSX.Element;
+export default _default;

package/esm/LinearSyntenyView/components/ImportForm.js

@@ -0,0 +1,99 @@
+import React, { useState, useEffect } from 'react';
+import { Button, Container, FormControl, FormLabel, FormControlLabel, Grid, Paper, Radio, RadioGroup, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util';
+import { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui';
+import ImportCustomTrack from './ImportCustomTrack';
+import ImportSyntenyTrackSelector from './ImportSyntenyTrackSelector';
+const useStyles = makeStyles()(theme => ({
+    importFormContainer: {
+        padding: theme.spacing(4),
+        margin: '0 auto',
+    },
+    assemblySelector: {
+        width: '75%',
+        margin: '0 auto',
+    },
+}));
+function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData, assembly1, assembly2, model, }) {
+    const [choice, setChoice] = useState('none');
+    useEffect(() => {
+        if (choice === 'none') {
+            setSessionTrackData(undefined);
+            setShowTrackId(undefined);
+        }
+    }, [choice, setSessionTrackData, setShowTrackId]);
+    return (React.createElement(React.Fragment, null,
+        React.createElement(FormControl, null,
+            React.createElement(FormLabel, { id: "group-label" }, "(Optional) Select or add a synteny track"),
+            React.createElement(RadioGroup, { row: true, value: choice, onChange: event => setChoice(event.target.value), "aria-labelledby": "group-label" },
+                React.createElement(FormControlLabel, { value: "none", control: React.createElement(Radio, null), label: "None" }),
+                React.createElement(FormControlLabel, { value: "tracklist", control: React.createElement(Radio, null), label: "Existing track" }),
+                React.createElement(FormControlLabel, { value: "custom", control: React.createElement(Radio, null), label: "New track" }))),
+        choice === 'custom' ? (React.createElement(ImportCustomTrack, { setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, assembly2: assembly2, assembly1: assembly1 })) : null,
+        choice === 'tracklist' ? (React.createElement(ImportSyntenyTrackSelector, { model: model, assembly1: assembly1, assembly2: assembly2, setShowTrackId: setShowTrackId })) : null));
+}
+export default observer(function ({ model, }) {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const { assemblyNames } = session;
+    const [assembly2, setAssembly2] = useState(assemblyNames[0] || '');
+    const [assembly1, setAssembly1] = useState(assemblyNames[0] || '');
+    const [error, setError] = useState();
+    const [sessionTrackData, setSessionTrackData] = useState();
+    const [showTrackId, setShowTrackId] = useState();
+    async function onOpenClick() {
+        try {
+            if (!isSessionWithAddTracks(session)) {
+                return;
+            }
+            setError(undefined);
+            const { assemblyManager } = session;
+            const assemblies = [assembly1, assembly2];
+            model.setViews(await Promise.all(assemblies.map(async (sel) => {
+                const asm = await assemblyManager.waitForAssembly(sel);
+                if (!asm) {
+                    throw new Error(`Assembly ${sel} failed to load`);
+                }
+                return {
+                    type: 'LinearGenomeView',
+                    bpPerPx: 1,
+                    offsetPx: 0,
+                    hideHeader: true,
+                    displayedRegions: asm.regions,
+                };
+            })));
+            model.views.forEach(view => view.setWidth(model.width));
+            if (sessionTrackData) {
+                session.addTrackConf(sessionTrackData);
+                model.toggleTrack(sessionTrackData.trackId);
+            }
+            else if (showTrackId) {
+                model.showTrack(showTrackId);
+            }
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }
+    // this is a combination of any displayed error message we have
+    const displayError = error;
+    return (React.createElement(Container, { className: classes.importFormContainer },
+        displayError ? React.createElement(ErrorMessage, { error: displayError }) : null,
+        React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", className: classes.assemblySelector },
+            React.createElement(Grid, { item: true },
+                React.createElement(Paper, { style: { padding: 12 } },
+                    React.createElement("p", { style: { textAlign: 'center' } }, "Select assemblies for linear synteny view"),
+                    React.createElement(Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
+                        React.createElement(Grid, { item: true },
+                            React.createElement(AssemblySelector, { selected: assembly1, onChange: val => setAssembly1(val), session: session })),
+                        React.createElement(Grid, { item: true },
+                            React.createElement(AssemblySelector, { selected: assembly2, onChange: val => setAssembly2(val), session: session })),
+                        React.createElement(Grid, { item: true },
+                            React.createElement(FormControl, null,
+                                React.createElement(Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),
+                React.createElement(TrackSelector, { setShowTrackId: setShowTrackId, assembly2: assembly2, assembly1: assembly1, setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, model: model })))));
+});
+//# sourceMappingURL=ImportForm.js.map

package/esm/LinearSyntenyView/components/ImportForm.js.map

@@ -0,0 +1 @@
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package/esm/LinearSyntenyView/components/ImportSyntenyTrackSelector.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { LinearSyntenyViewModel } from '../model';
+declare const Selector: ({ model, assembly1, assembly2, setShowTrackId, }: {
+    model: LinearSyntenyViewModel;
+    assembly1: string;
+    assembly2: string;
+    setShowTrackId: (arg: string) => void;
+}) => React.JSX.Element;
+export default Selector;

package/esm/LinearSyntenyView/components/ImportSyntenyTrackSelector.js

@@ -0,0 +1,38 @@
+import React, { useState, useEffect } from 'react';
+import { Select, MenuItem, Paper, Typography } from '@mui/material';
+import { getSession } from '@jbrowse/core/util';
+import { getTrackName } from '@jbrowse/core/util/tracks';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { observer } from 'mobx-react';
+function f(track, assembly1, assembly2) {
+    const assemblyNames = readConfObject(track, 'assemblyNames');
+    return (assemblyNames.includes(assembly1) &&
+        assemblyNames.includes(assembly2) &&
+        track.type.includes('Synteny'));
+}
+const Selector = observer(({ model, assembly1, assembly2, setShowTrackId, }) => {
+    var _a;
+    const session = getSession(model);
+    const { tracks = [], sessionTracks = [] } = session;
+    const allTracks = [...tracks, ...sessionTracks];
+    const filteredTracks = allTracks.filter(t => f(t, assembly2, assembly1));
+    const resetTrack = ((_a = filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.trackId) || '';
+    const [value, setValue] = useState(resetTrack);
+    useEffect(() => {
+        // if assembly1/assembly2 changes, then we will want to use this effect to
+        // change the state of the useState because it otherwise gets locked to a
+        // stale value
+        setValue(resetTrack);
+    }, [resetTrack]);
+    useEffect(() => {
+        // sets track data in a useEffect because the initial load is needed as well
+        // as onChange's to the select box
+        setShowTrackId(value);
+    }, [value, setShowTrackId]);
+    return (React.createElement(Paper, { style: { padding: 12 } },
+        React.createElement(Typography, { paragraph: true }, "Select a track from the select box below, the track will be shown when you hit \"Launch\"."),
+        filteredTracks.length ? (React.createElement(Select, { value: value, onChange: event => setValue(event.target.value) }, filteredTracks.map(track => (React.createElement(MenuItem, { key: track.trackId, value: track.trackId }, getTrackName(track, session)))))) : (React.createElement(ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
+});
+export default Selector;
+//# sourceMappingURL=ImportSyntenyTrackSelector.js.map

package/esm/LinearSyntenyView/components/ImportSyntenyTrackSelector.js.map

@@ -0,0 +1 @@
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package/esm/LinearSyntenyView/components/LinearSyntenyView.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { LinearSyntenyViewModel } from '../model';
+type LSV = LinearSyntenyViewModel;
+declare const LinearSyntenyView: ({ model }: {
+    model: LSV;
+}) => React.JSX.Element;
+export default LinearSyntenyView;

package/esm/LinearSyntenyView/components/LinearSyntenyView.js

@@ -0,0 +1,10 @@
+import React, { lazy } from 'react';
+import { observer } from 'mobx-react';
+// locals
+import LinearComparativeViewComponent from '../../LinearComparativeView/components/LinearComparativeView';
+const ImportForm = lazy(() => import('./ImportForm'));
+const LinearSyntenyView = observer(({ model }) => {
+    return !model.initialized ? (React.createElement(ImportForm, { model: model })) : (React.createElement(LinearComparativeViewComponent, { model: model }));
+});
+export default LinearSyntenyView;
+//# sourceMappingURL=LinearSyntenyView.js.map

package/esm/LinearSyntenyView/components/LinearSyntenyView.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"LinearSyntenyView.js","sourceRoot":"","sources":["../../../src/LinearSyntenyView/components/LinearSyntenyView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,SAAS;AACT,OAAO,8BAA8B,MAAM,8DAA8D,CAAA;AAGzG,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,CAAA;AAIrD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IAC/D,OAAO,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAC1B,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC7B,CAAC,CAAC,CAAC,CACF,oBAAC,8BAA8B,IAAC,KAAK,EAAE,KAAK,GAAI,CACjD,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/esm/LinearSyntenyView/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LinearSyntenyView/index.js

@@ -0,0 +1,14 @@
+import { lazy } from 'react';
+import modelFactory from './model';
+import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
+export default (pluginManager) => {
+    pluginManager.addViewType(() => {
+        return new ViewType({
+            name: 'LinearSyntenyView',
+            displayName: 'Linear synteny view',
+            stateModel: modelFactory(pluginManager),
+            ReactComponent: lazy(() => import('./components/LinearSyntenyView')),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/LinearSyntenyView/index.js.map

@@ -0,0 +1 @@
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