@jbrowse/plugin-linear-comparative-view 2.18.0 → 3.0.1

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

@@ -1,169 +0,0 @@
-import React, { useEffect, useState } from 'react';
-import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
-import { FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
-import { observer } from 'mobx-react';
-import { basename, extName, getName, stripGz } from './util';
-function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, 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 if (radioOption === '.pif.gz') {
-        return {
-            type: 'PairwiseIndexedPAFAdapter',
-            pifGzLocation: fileLocation,
-            index: { location: indexFileLocation },
-            assemblyNames: [assembly1, assembly2],
-        };
-    }
-    else {
-        throw new Error(`Unknown to detect type ${radioOption} from filename (select radio button to clarify)`);
-    }
-}
-const ImportCustomTrack = observer(function ({ assembly1, assembly2, setUserOpenedSyntenyTrack, }) {
-    const [bed2Location, setBed2Location] = useState();
-    const [bed1Location, setBed1Location] = useState();
-    const [fileLocation, setFileLocation] = useState();
-    const [indexFileLocation, setIndexFileLocation] = useState();
-    const [value, setValue] = useState('');
-    const [error, setError] = useState();
-    const fileName = getName(fileLocation);
-    const radioOption = value || (fileName ? extName(stripGz(fileName)) : '');
-    useEffect(() => {
-        try {
-            if (fileLocation) {
-                const fn = fileName ? basename(fileName) : 'MyTrack';
-                const trackId = `${fn}-${Date.now()}`;
-                setError(undefined);
-                setUserOpenedSyntenyTrack({
-                    trackId,
-                    name: fn,
-                    assemblyNames: [assembly2, assembly1],
-                    type: 'SyntenyTrack',
-                    adapter: getAdapter({
-                        radioOption,
-                        assembly1,
-                        assembly2,
-                        fileLocation,
-                        indexFileLocation,
-                        bed1Location,
-                        bed2Location,
-                    }),
-                });
-            }
-        }
-        catch (e) {
-            console.error(e);
-            setError(e);
-        }
-    }, [
-        fileName,
-        assembly1,
-        assembly2,
-        bed1Location,
-        bed2Location,
-        fileLocation,
-        indexFileLocation,
-        radioOption,
-        setUserOpenedSyntenyTrack,
-    ]);
-    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. 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, { item: true },
-                    React.createElement(FormControlLabel, { value: ".pif.gz", control: React.createElement(Radio, null), label: ".pif.gz" })))),
-        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);
-                            } }))))) : value === '.pif.gz' ? (React.createElement("div", { style: { display: 'flex' } },
-                React.createElement("div", null,
-                    React.createElement(FileSelector, { name: `${value} location`, description: "", location: fileLocation, setLocation: loc => {
-                            setFileLocation(loc);
-                        } })),
-                React.createElement("div", null,
-                    React.createElement(FileSelector, { name: `${value} index location`, description: "", location: indexFileLocation, setLocation: loc => {
-                            setIndexFileLocation(loc);
-                        } })))) : (React.createElement(FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
-                    setFileLocation(loc);
-                } }))))));
-});
-export default ImportCustomTrack;

package/esm/LinearSyntenyView/components/ImportForm/Spacer.d.ts

@@ -1,2 +0,0 @@
-import React from 'react';
-export default function Spacer(): React.JSX.Element;

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

@@ -1,4 +0,0 @@
-import React from 'react';
-export default function Spacer() {
-    return React.createElement("div", { style: { flexGrow: 1 } });
-}

package/esm/LinearSyntenyView/components/ImportForm/TrackSelector.d.ts

@@ -1,10 +0,0 @@
-import React from 'react';
-import type { LinearSyntenyViewModel } from '../../model';
-declare const ImportSyntenyTrackSelector: ({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, }: {
-    model: LinearSyntenyViewModel;
-    assembly1: string;
-    assembly2: string;
-    preConfiguredSyntenyTrack: string | undefined;
-    setPreConfiguredSyntenyTrack: (arg: string) => void;
-}) => React.JSX.Element;
-export default ImportSyntenyTrackSelector;

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

@@ -1,32 +0,0 @@
-import React, { useEffect, useState } from 'react';
-import { readConfObject } from '@jbrowse/core/configuration';
-import { ErrorMessage } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
-import { getTrackName } from '@jbrowse/core/util/tracks';
-import { MenuItem, Paper, Select, Typography } from '@mui/material';
-import { observer } from 'mobx-react';
-const ImportSyntenyTrackSelector = observer(function ({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, }) {
-    var _a;
-    const session = getSession(model);
-    const { tracks = [], sessionTracks = [] } = session;
-    const allTracks = [...tracks, ...sessionTracks];
-    const filteredTracks = allTracks.filter(track => {
-        const assemblyNames = readConfObject(track, 'assemblyNames');
-        return (assemblyNames.includes(assembly1) &&
-            assemblyNames.includes(assembly2) &&
-            track.type.includes('Synteny'));
-    });
-    const resetTrack = ((_a = filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.trackId) || '';
-    const [value, setValue] = useState(resetTrack);
-    useEffect(() => {
-        if (value !== preConfiguredSyntenyTrack) {
-            setPreConfiguredSyntenyTrack(value);
-        }
-    }, [value, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack]);
-    return (React.createElement(Paper, { style: { padding: 12 } },
-        React.createElement(Typography, null, "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 ImportSyntenyTrackSelector;

package/esm/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.d.ts

@@ -1,14 +0,0 @@
-import React from 'react';
-import type { LinearSyntenyViewModel } from '../../model';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { SnapshotIn } from 'mobx-state-tree';
-type Conf = SnapshotIn<AnyConfigurationModel>;
-export default function TrackSelector({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack, }: {
-    model: LinearSyntenyViewModel;
-    assembly1: string;
-    assembly2: string;
-    preConfiguredSyntenyTrack: string | undefined;
-    setUserOpenedSyntenyTrack: (arg: Conf) => void;
-    setPreConfiguredSyntenyTrack: (arg?: string) => void;
-}): React.JSX.Element;
-export {};

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

@@ -1,23 +0,0 @@
-import React, { useEffect, useState } from 'react';
-import { FormControl, FormControlLabel, Radio, RadioGroup } from '@mui/material';
-import ImportCustomTrack from './AddCustomTrack';
-import ImportSyntenyTrackSelector from './TrackSelector';
-export default function TrackSelector({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack, }) {
-    const [choice, setChoice] = useState('tracklist');
-    useEffect(() => {
-        if (choice === 'none') {
-            setPreConfiguredSyntenyTrack(undefined);
-            setUserOpenedSyntenyTrack(undefined);
-        }
-    }, [choice, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack]);
-    return (React.createElement("div", null,
-        React.createElement(FormControl, null,
-            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, { setUserOpenedSyntenyTrack: setUserOpenedSyntenyTrack, assembly2: assembly2, assembly1: assembly1 })) : null,
-        choice === 'tracklist' ? (React.createElement(ImportSyntenyTrackSelector, { key: `${assembly1}-${assembly2}`, model: model, assembly1: assembly1, assembly2: assembly2, preConfiguredSyntenyTrack: preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack: setPreConfiguredSyntenyTrack })) : null));
-}