@jbrowse/plugin-linear-genome-view/esm/LinearGenomeView/components/SequenceSearchDialog.js

JBrowse 2 linear genome view

import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
import { useState } from 'react';
import { Dialog } from '@jbrowse/core/ui';
import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util';
import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, FormGroup, TextField, Typography, } from '@mui/material';
import { observer } from 'mobx-react';
import { getSnapshot } from 'mobx-state-tree';
import { makeStyles } from 'tss-react/mui';
const useStyles = makeStyles()({
    dialogContent: {
        width: '40em',
    },
});
const SequenceSearchDialog = observer(function ({ model, handleClose, }) {
    const { classes } = useStyles();
    const [value, setValue] = useState('');
    const [searchForward, setSearchForward] = useState(true);
    const [searchReverse, setSearchReverse] = useState(true);
    const [caseInsensitive, setCaseInsensitive] = useState(true);
    let error;
    try {
        new RegExp(value);
    }
    catch (e) {
        error = e;
    }
    return (_jsxs(Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Sequence search", children: [_jsxs(DialogContent, { className: classes.dialogContent, children: [_jsx(Typography, { children: "Supply a sequence to search for. A track will be created with the resulting matches once submitted. You can also supply regex style expressions e.g. AACT(C|T)." }), _jsx(TextField, { value: value, onChange: e => {
                            setValue(e.target.value);
                        }, helperText: "Sequence search pattern" }), _jsxs(FormGroup, { children: [_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: searchForward, onChange: event => {
                                        setSearchForward(event.target.checked);
                                    } }), label: "Search forward strand" }), _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: searchReverse, onChange: event => {
                                        setSearchReverse(event.target.checked);
                                    } }), label: "Search reverse strand" }), _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: caseInsensitive, onChange: event => {
                                        setCaseInsensitive(event.target.checked);
                                    } }), label: "Case insensitive" })] }), error ? _jsx(Typography, { color: "error", children: `${error}` }) : null] }), _jsxs(DialogActions, { children: [_jsx(Button, { onClick: () => {
                            var _a;
                            if (value) {
                                const trackId = `sequence_search_${+Date.now()}`;
                                const session = getSession(model);
                                const { assemblyManager } = session;
                                const assemblyName = model.assemblyNames[0];
                                if (isSessionWithAddTracks(session)) {
                                    session.addTrackConf({
                                        trackId,
                                        name: `Sequence search ${value}`,
                                        assemblyNames: [assemblyName],
                                        type: 'FeatureTrack',
                                        adapter: {
                                            type: 'SequenceSearchAdapter',
                                            search: value,
                                            searchForward,
                                            searchReverse,
                                            caseInsensitive,
                                            sequenceAdapter: getSnapshot((_a = assemblyManager.get(assemblyName)) === null || _a === void 0 ? void 0 : _a.configuration.sequence.adapter),
                                        },
                                    });
                                    model.showTrack(trackId);
                                }
                            }
                            handleClose();
                        }, variant: "contained", color: "primary", children: "Submit" }), _jsx(Button, { onClick: () => {
                            handleClose();
                        }, variant: "contained", color: "secondary", children: "Close" })] })] }));
});
export default SequenceSearchDialog;