@jbrowse/plugin-linear-comparative-view 2.18.0 → 3.0.0

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

@@ -0,0 +1,125 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
+import HelpIcon from '@mui/icons-material/Help';
+import { Button, FormControlLabel, Grid2, Paper, Radio, RadioGroup, Tooltip, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { getAdapter } from './getAdapter';
+import { basename, extName, getName, stripGz } from './util';
+const ImportSyntenyOpenCustomTrack = observer(function ({ model, assembly1, assembly2, selectedRow, }) {
+    const [swap, setSwap] = useState(false);
+    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()}-sessionTrack`;
+                setError(undefined);
+                model.setImportFormSyntenyTrack(selectedRow, {
+                    type: 'userOpened',
+                    value: {
+                        trackId,
+                        name: fn,
+                        assemblyNames: [assembly2, assembly1],
+                        type: 'SyntenyTrack',
+                        adapter: getAdapter({
+                            radioOption,
+                            assembly1: swap ? assembly2 : assembly1,
+                            assembly2: swap ? assembly1 : assembly2,
+                            fileLocation,
+                            indexFileLocation,
+                            bed1Location,
+                            bed2Location,
+                        }),
+                    },
+                });
+            }
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }, [
+        swap,
+        model,
+        selectedRow,
+        fileName,
+        assembly1,
+        assembly2,
+        bed1Location,
+        bed2Location,
+        fileLocation,
+        indexFileLocation,
+        radioOption,
+    ]);
+    const helpStrings = {
+        '.paf': 'minimap2 target.fa query.fa',
+        '.pif.gz': 'minimap2 target.fa query.fa',
+        '.out': 'mashmap target.fa query.fa',
+        '.delta': 'mummer target.fa query.fa',
+        '.chain': 'e.g. queryToTarget.chain',
+    };
+    return (_jsxs(Paper, { style: { padding: 12 }, children: [error ? _jsx(ErrorMessage, { error: error }) : null, _jsx(Typography, { style: { textAlign: 'center' }, children: "Add a .paf (minimap2), .delta (Mummer), .chain (UCSC liftover), .anchors or .anchors.simple (MCScan), or .pif.gz (jbrowse CLI make-pif) file to view. These file types can also be gzipped." }), _jsx(RadioGroup, { value: radioOption, onChange: event => {
+                    setValue(event.target.value);
+                }, children: _jsx(Grid2, { container: true, justifyContent: "center", children: [
+                        '.paf',
+                        '.delta',
+                        '.out',
+                        '.chain',
+                        '.anchors',
+                        '.anchors.simple',
+                        '.pif.gz',
+                    ].map(extension => (_jsx(FormControlLabel, { value: extension, control: _jsx(Radio, {}), label: extension }, extension))) }) }), _jsx(Grid2, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
+                    radioOption === '.out' ||
+                    radioOption === '.delta' ||
+                    radioOption === '.chain' ||
+                    radioOption === '.pif.gz' ? (_jsxs("div", { style: {
+                        display: 'flex',
+                        flexDirection: 'column',
+                        gap: 10,
+                    }, children: [_jsx(FileSelector, { name: `${radioOption} location`, inline: true, description: "", location: fileLocation, setLocation: loc => {
+                                setFileLocation(loc);
+                            } }), _jsxs("div", { children: [_jsxs("div", { children: ["Verify or click swap", _jsx(Tooltip, { title: _jsx("code", { children: helpStrings[radioOption] }), children: _jsx(HelpIcon, {}) })] }), _jsxs("div", { style: {
+                                        display: 'flex',
+                                        gap: 20,
+                                    }, children: [_jsxs("div", { style: {
+                                                display: 'grid',
+                                                gridTemplateColumns: '1fr 1fr',
+                                                gap: 4,
+                                                alignItems: 'center',
+                                            }, children: [_jsx("div", { children: _jsx("i", { children: swap ? assembly2 : assembly1 }) }), _jsx("div", { children: "query assembly" }), _jsx("div", { children: _jsx("i", { children: swap ? assembly1 : assembly2 }) }), _jsx("div", { children: "target assembly" })] }), _jsx(Button, { variant: "contained", onClick: () => {
+                                                setSwap(!swap);
+                                            }, children: "Swap?" })] })] })] })) : value === '.anchors' || value === '.anchors.simple' ? (_jsxs("div", { children: [_jsxs("div", { style: { margin: 20 }, children: ["Open the ", value, " and .bed files for both genome assemblies from the MCScan (Python version) pipeline", ' ', _jsx("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)", children: "(more info)" })] }), _jsxs("div", { children: [_jsx(FileSelector, { inline: true, name: value, location: fileLocation, setLocation: loc => {
+                                        setFileLocation(loc);
+                                    } }), _jsx(FileSelector, { inline: true, name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => {
+                                        setBed1Location(loc);
+                                    } }), _jsx(FileSelector, { inline: true, name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
+                                        setBed2Location(loc);
+                                    } })] }), _jsxs("div", { style: {
+                                margin: 'auto',
+                                display: 'flex',
+                                justifyContent: 'center',
+                                gap: 20,
+                            }, children: [_jsxs("div", { style: {
+                                        display: 'grid',
+                                        gridTemplateColumns: '1fr 1fr',
+                                        gap: 4,
+                                        alignItems: 'center',
+                                    }, children: [_jsx("div", { children: _jsx("i", { children: swap ? assembly2 : assembly1 }) }), _jsx("div", { children: "bed1 assembly" }), _jsx("div", { children: _jsx("i", { children: swap ? assembly1 : assembly2 }) }), _jsx("div", { children: "bed2 assembly" })] }), _jsx(Button, { variant: "contained", onClick: () => {
+                                        setSwap(!swap);
+                                    }, children: "Swap?" })] })] })) : value === '.pif.gz' ? (_jsxs("div", { style: { display: 'flex' }, children: [_jsx("div", { children: _jsx(FileSelector, { name: `${value} location`, description: "", location: fileLocation, setLocation: loc => {
+                                    setFileLocation(loc);
+                                } }) }), _jsx("div", { children: _jsx(FileSelector, { name: `${value} index location`, description: "", location: indexFileLocation, setLocation: loc => {
+                                    setIndexFileLocation(loc);
+                                } }) })] })) : (_jsx(FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
+                        setFileLocation(loc);
+                    } })) })] }));
+});
+export default ImportSyntenyOpenCustomTrack;

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

@@ -0,0 +1,8 @@
+import type { LinearSyntenyViewModel } from '../../model';
+declare const ImportSyntenyTrackSelector: ({ model, selectedRow, assembly1, assembly2, }: {
+    model: LinearSyntenyViewModel;
+    selectedRow: number;
+    assembly1: string;
+    assembly2: string;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ImportSyntenyTrackSelector;

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

@@ -0,0 +1,37 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect } 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, selectedRow, assembly1, assembly2, }) {
+    var _a;
+    const session = getSession(model);
+    const { importFormSyntenyTrackSelections } = 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 r = importFormSyntenyTrackSelections[selectedRow];
+    const value = (r === null || r === void 0 ? void 0 : r.type) === 'preConfigured' ? r.value : undefined;
+    useEffect(() => {
+        model.setImportFormSyntenyTrack(selectedRow, {
+            type: 'preConfigured',
+            value: resetTrack,
+        });
+    }, [assembly2, assembly1, resetTrack, selectedRow, model]);
+    return (_jsxs(Paper, { style: { padding: 12 }, children: [_jsx(Typography, { children: "Select a track from the select box below, the track will be shown when you hit \"Launch\"." }), value && filteredTracks.map(r => r.trackId).includes(value) ? (_jsx(Select, { value: value, onChange: event => {
+                    model.setImportFormSyntenyTrack(selectedRow, {
+                        type: 'preConfigured',
+                        value: event.target.value,
+                    });
+                }, children: filteredTracks.map(track => (_jsx(MenuItem, { value: track.trackId, children: getTrackName(track, session) }, track.trackId))) })) : (_jsx(ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))] }));
+});
+export default ImportSyntenyTrackSelector;

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

@@ -0,0 +1,7 @@
+import type { LinearSyntenyViewModel } from '../../model';
+export default function ImportSyntenyTrackSelectorArea({ model, assembly1, assembly2, selectedRow, }: {
+    model: LinearSyntenyViewModel;
+    assembly1: string;
+    assembly2: string;
+    selectedRow: number;
+}): import("react/jsx-runtime").JSX.Element;

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

@@ -0,0 +1,16 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { FormControl, FormControlLabel, Radio, RadioGroup } from '@mui/material';
+import ImportCustomTrack from './ImportSyntenyOpenCustomTrack';
+import ImportSyntenyTrackSelector from './ImportSyntenyPreConfigured';
+export default function ImportSyntenyTrackSelectorArea({ model, assembly1, assembly2, selectedRow, }) {
+    const [choice, setChoice] = useState('tracklist');
+    useEffect(() => {
+        if (choice === 'none') {
+            model.setImportFormSyntenyTrack(selectedRow, { type: 'none' });
+        }
+    }, [choice, model, selectedRow]);
+    return (_jsxs("div", { children: [_jsx(FormControl, { children: _jsxs(RadioGroup, { row: true, value: choice, "aria-labelledby": "group-label", onChange: event => {
+                        setChoice(event.target.value);
+                    }, children: [_jsx(FormControlLabel, { value: "none", control: _jsx(Radio, {}), label: "None" }), _jsx(FormControlLabel, { value: "tracklist", control: _jsx(Radio, {}), label: "Existing track" }), _jsx(FormControlLabel, { value: "custom", control: _jsx(Radio, {}), label: "New track" })] }) }), choice === 'custom' ? (_jsx(ImportCustomTrack, { model: model, selectedRow: selectedRow, assembly2: assembly2, assembly1: assembly1 })) : null, choice === 'tracklist' ? (_jsx(ImportSyntenyTrackSelector, { model: model, selectedRow: selectedRow, assembly1: assembly1, assembly2: assembly2 })) : null] }));
+}

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

@@ -1,6 +1,5 @@
-import React from 'react';
 import type { LinearSyntenyViewModel } from '../../model';
 declare const LinearSyntenyViewImportForm: ({ model, }: {
     model: LinearSyntenyViewModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default LinearSyntenyViewImportForm;

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

@@ -1,13 +1,14 @@
-import React, { useState } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import { AssemblySelector, ErrorMessage } from '@jbrowse/core/ui';
-import { getSession, isSessionWithAddTracks, notEmpty, } from '@jbrowse/core/util';
+import { getSession, notEmpty } from '@jbrowse/core/util';
 import ArrowForwardIosIcon from '@mui/icons-material/ArrowForwardIos';
 import CloseIcon from '@mui/icons-material/Close';
 import { Button, Container, IconButton } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import Spacer from './Spacer';
-import TrackSelector from './TrackSelectorUtil';
+import ImportSyntenyTrackSelector from './ImportSyntenyTrackSelectorArea';
+import { doSubmit } from './doSubmit';
 const useStyles = makeStyles()(theme => ({
     importFormContainer: {
         padding: theme.spacing(4),
@@ -24,6 +25,7 @@ const useStyles = makeStyles()(theme => ({
     },
     flex: {
         display: 'flex',
+        gap: 90,
     },
     mb: {
         marginBottom: 10,
@@ -31,8 +33,12 @@ const useStyles = makeStyles()(theme => ({
     bg: {
         background: theme.palette.divider,
     },
-    fixedWidth: {
-        width: 700,
+    rightPanel: {
+        flexGrow: 11,
+    },
+    leftPanel: {
+        flexGrow: 4,
+        flexShrink: 0,
     },
 }));
 const LinearSyntenyViewImportForm = observer(function ({ model, }) {
@@ -46,120 +52,38 @@ const LinearSyntenyViewImportForm = observer(function ({ model, }) {
         defaultAssemblyName,
     ]);
     const [error, setError] = useState();
-    const [userOpenedSyntenyTracksToShow, setUserOpenedSyntenyTracksToShow] = useState([]);
-    const [preConfiguredSyntenyTracksToShow, setPreConfiguredSyntenyTracksToShow,] = useState([]);
-    return (React.createElement(Container, { className: classes.importFormContainer },
-        error ? React.createElement(ErrorMessage, { error: error }) : null,
-        React.createElement("div", { className: classes.flex },
-            React.createElement(Spacer, null),
-            React.createElement("div", null,
-                React.createElement("div", { className: classes.mb }, "Select assemblies for linear synteny view"),
-                selectedAssemblyNames.map((assemblyName, idx) => (React.createElement("div", { key: `${assemblyName}-${idx}`, className: classes.rel },
-                    React.createElement("span", null,
-                        "Row ",
-                        idx + 1,
-                        ": "),
-                    React.createElement(IconButton, { disabled: selectedAssemblyNames.length <= 2, onClick: () => {
-                            setSelectedAssemblyNames(selectedAssemblyNames
-                                .map((asm, idx2) => (idx2 === idx ? undefined : asm))
-                                .filter(notEmpty));
-                            setPreConfiguredSyntenyTracksToShow(preConfiguredSyntenyTracksToShow
-                                .map((asm, idx2) => (idx2 === idx ? undefined : asm))
-                                .filter(notEmpty));
-                            setUserOpenedSyntenyTracksToShow(userOpenedSyntenyTracksToShow
-                                .map((asm, idx2) => (idx2 === idx ? undefined : asm))
-                                .filter(notEmpty));
-                            if (selectedRow >= selectedAssemblyNames.length - 2) {
-                                setSelectedRow(0);
-                            }
-                        } },
-                        React.createElement(CloseIcon, null)),
-                    React.createElement(AssemblySelector, { helperText: "", selected: assemblyName, onChange: newAssembly => {
-                            setSelectedAssemblyNames(selectedAssemblyNames.map((asm, idx2) => idx2 === idx ? newAssembly : asm));
-                        }, session: session }),
-                    idx !== selectedAssemblyNames.length - 1 ? (React.createElement(IconButton, { className: cx(classes.synbutton, idx === selectedRow ? classes.bg : undefined), onClick: () => {
-                            setSelectedRow(idx);
-                        } },
-                        React.createElement(ArrowForwardIosIcon, null))) : null))),
-                React.createElement("div", null,
-                    React.createElement(Button, { className: classes.button, variant: "contained", color: "secondary", onClick: () => {
-                            setSelectedAssemblyNames([
-                                ...selectedAssemblyNames,
-                                defaultAssemblyName,
-                            ]);
-                        } }, "Add row"),
-                    React.createElement(Button, { className: classes.button, onClick: () => {
-                            ;
-                            (async () => {
-                                try {
-                                    setError(undefined);
-                                    await doSubmit({
-                                        userOpenedSyntenyTracksToShow,
-                                        preConfiguredSyntenyTracksToShow,
-                                        selectedAssemblyNames,
-                                        model,
-                                    });
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    setError(e);
-                                }
-                            })();
-                        }, variant: "contained", color: "primary" }, "Launch"))),
-            React.createElement(Spacer, null),
-            React.createElement("div", { className: classes.fixedWidth },
-                React.createElement("div", null,
-                    "Synteny dataset to display between row ",
-                    selectedRow + 1,
-                    " and",
-                    ' ',
-                    selectedRow + 2),
-                React.createElement(TrackSelector, { model: model, preConfiguredSyntenyTrack: preConfiguredSyntenyTracksToShow[selectedRow], assembly1: selectedAssemblyNames[selectedRow], assembly2: selectedAssemblyNames[selectedRow + 1], setPreConfiguredSyntenyTrack: arg => {
-                        const clone = [...preConfiguredSyntenyTracksToShow];
-                        clone[selectedRow] = arg;
-                        setPreConfiguredSyntenyTracksToShow(clone);
-                    }, setUserOpenedSyntenyTrack: arg => {
-                        const clone = [...userOpenedSyntenyTracksToShow];
-                        clone[selectedRow] = arg;
-                        setUserOpenedSyntenyTracksToShow(clone);
-                    } }))),
-        React.createElement(Spacer, null)));
+    return (_jsxs(Container, { className: classes.importFormContainer, children: [error ? _jsx(ErrorMessage, { error: error }) : null, _jsxs("div", { className: classes.flex, children: [_jsxs("div", { className: classes.leftPanel, children: [_jsx("div", { className: classes.mb, children: "Select assemblies for linear synteny view" }), selectedAssemblyNames.map((assemblyName, idx) => (_jsxs("div", { className: classes.rel, children: [_jsxs("span", { children: ["Row ", idx + 1, ": "] }), _jsx(IconButton, { disabled: selectedAssemblyNames.length <= 2, onClick: () => {
+                                            model.importFormRemoveRow(idx);
+                                            setSelectedAssemblyNames(selectedAssemblyNames
+                                                .map((asm, idx2) => (idx2 === idx ? undefined : asm))
+                                                .filter(notEmpty));
+                                            if (selectedRow >= selectedAssemblyNames.length - 2) {
+                                                setSelectedRow(0);
+                                            }
+                                        }, children: _jsx(CloseIcon, {}) }), _jsx(AssemblySelector, { helperText: "", selected: assemblyName, onChange: newAssembly => {
+                                            setSelectedAssemblyNames(selectedAssemblyNames.map((asm, idx2) => idx2 === idx ? newAssembly : asm));
+                                        }, session: session }), idx !== selectedAssemblyNames.length - 1 ? (_jsx(IconButton, { "data-testid": "synbutton", className: cx(classes.synbutton, idx === selectedRow ? classes.bg : undefined), onClick: () => {
+                                            setSelectedRow(idx);
+                                        }, children: _jsx(ArrowForwardIosIcon, {}) })) : null] }, `${assemblyName}-${idx}`))), _jsxs("div", { children: [_jsx(Button, { className: classes.button, variant: "contained", color: "secondary", onClick: () => {
+                                            setSelectedAssemblyNames([
+                                                ...selectedAssemblyNames,
+                                                defaultAssemblyName,
+                                            ]);
+                                        }, children: "Add row" }), _jsx(Button, { className: classes.button, onClick: () => {
+                                            ;
+                                            (async () => {
+                                                try {
+                                                    setError(undefined);
+                                                    await doSubmit({
+                                                        selectedAssemblyNames,
+                                                        model,
+                                                    });
+                                                }
+                                                catch (e) {
+                                                    console.error(e);
+                                                    setError(e);
+                                                }
+                                            })();
+                                        }, variant: "contained", color: "primary", children: "Launch" })] })] }), _jsxs("div", { className: classes.rightPanel, children: [_jsxs("div", { children: ["Synteny dataset to display between row ", selectedRow + 1, " and", ' ', selectedRow + 2] }), _jsx(ImportSyntenyTrackSelector, { model: model, selectedRow: selectedRow, assembly1: selectedAssemblyNames[selectedRow], assembly2: selectedAssemblyNames[selectedRow + 1] })] })] })] }));
 });
-async function doSubmit({ selectedAssemblyNames, model, preConfiguredSyntenyTracksToShow, userOpenedSyntenyTracksToShow, }) {
-    const session = getSession(model);
-    const { assemblyManager } = session;
-    model.setViews(await Promise.all(selectedAssemblyNames.map(async (assemblyName) => {
-        const asm = await assemblyManager.waitForAssembly(assemblyName);
-        if (!asm) {
-            throw new Error(`Assembly "${assemblyName}" failed to load`);
-        }
-        return {
-            type: 'LinearGenomeView',
-            bpPerPx: 1,
-            offsetPx: 0,
-            hideHeader: true,
-            displayedRegions: asm.regions,
-        };
-    })));
-    for (const view of model.views) {
-        view.setWidth(model.width);
-        view.showAllRegions();
-    }
-    if (!isSessionWithAddTracks(session)) {
-        session.notify("Can't add tracks", 'warning');
-    }
-    else {
-        userOpenedSyntenyTracksToShow.map((f, idx) => {
-            if (f) {
-                session.addTrackConf(f);
-                model.toggleTrack(f.trackId, idx);
-            }
-        });
-    }
-    preConfiguredSyntenyTracksToShow.map((f, idx) => {
-        if (f) {
-            model.showTrack(f, idx);
-        }
-    });
-}
 export default LinearSyntenyViewImportForm;

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

@@ -0,0 +1,5 @@
+import type { LinearSyntenyViewModel } from '../../model';
+export declare function doSubmit({ selectedAssemblyNames, model, }: {
+    selectedAssemblyNames: string[];
+    model: LinearSyntenyViewModel;
+}): Promise<void>;

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

@@ -0,0 +1,40 @@
+import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util';
+import { toJS } from 'mobx';
+export async function doSubmit({ selectedAssemblyNames, model, }) {
+    const session = getSession(model);
+    const { assemblyManager } = session;
+    const { importFormSyntenyTrackSelections } = model;
+    model.setViews(await Promise.all(selectedAssemblyNames.map(async (assemblyName) => {
+        const asm = await assemblyManager.waitForAssembly(assemblyName);
+        if (!asm) {
+            throw new Error(`Assembly "${assemblyName}" failed to load`);
+        }
+        return {
+            type: 'LinearGenomeView',
+            bpPerPx: 1,
+            offsetPx: 0,
+            hideHeader: true,
+            displayedRegions: asm.regions,
+        };
+    })));
+    for (const view of model.views) {
+        view.setWidth(model.width);
+        view.showAllRegions();
+    }
+    if (!isSessionWithAddTracks(session)) {
+        session.notify("Can't add tracks", 'warning');
+    }
+    else {
+        toJS(importFormSyntenyTrackSelections).map((f, idx) => {
+            var _a;
+            if (f.type === 'userOpened') {
+                session.addTrackConf(f.value);
+                model.toggleTrack((_a = f.value) === null || _a === void 0 ? void 0 : _a.trackId, idx);
+            }
+            else if (f.type === 'preConfigured') {
+                model.showTrack(f.value, idx);
+            }
+        });
+    }
+    model.clearImportFormSyntenyTracks();
+}

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

@@ -0,0 +1,117 @@
+import type { FileLocation } from '@jbrowse/core/util';
+export declare function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, bed1Location, bed2Location, }: {
+    radioOption: string;
+    assembly1: string;
+    assembly2: string;
+    fileLocation?: FileLocation;
+    indexFileLocation?: FileLocation;
+    bed1Location?: FileLocation;
+    bed2Location?: FileLocation;
+}): {
+    type: string;
+    pafLocation: FileLocation | undefined;
+    queryAssembly: string;
+    targetAssembly: string;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    assemblyNames?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    outLocation: FileLocation | undefined;
+    queryAssembly: string;
+    targetAssembly: string;
+    pafLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    assemblyNames?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    deltaLocation: FileLocation | undefined;
+    queryAssembly: string;
+    targetAssembly: string;
+    pafLocation?: undefined;
+    outLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    assemblyNames?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    chainLocation: FileLocation | undefined;
+    queryAssembly: string;
+    targetAssembly: string;
+    pafLocation?: undefined;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    assemblyNames?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    mcscanAnchorsLocation: FileLocation | undefined;
+    bed1Location: FileLocation | undefined;
+    bed2Location: FileLocation | undefined;
+    assemblyNames: string[];
+    pafLocation?: undefined;
+    queryAssembly?: undefined;
+    targetAssembly?: undefined;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    mcscanSimpleAnchorsLocation: FileLocation | undefined;
+    bed1Location: FileLocation | undefined;
+    bed2Location: FileLocation | undefined;
+    assemblyNames: string[];
+    pafLocation?: undefined;
+    queryAssembly?: undefined;
+    targetAssembly?: undefined;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    pifGzLocation?: undefined;
+    index?: undefined;
+} | {
+    type: string;
+    pifGzLocation: FileLocation | undefined;
+    index: {
+        location: FileLocation | undefined;
+    };
+    assemblyNames: string[];
+    pafLocation?: undefined;
+    queryAssembly?: undefined;
+    targetAssembly?: undefined;
+    outLocation?: undefined;
+    deltaLocation?: undefined;
+    chainLocation?: undefined;
+    mcscanAnchorsLocation?: undefined;
+    bed1Location?: undefined;
+    bed2Location?: undefined;
+    mcscanSimpleAnchorsLocation?: undefined;
+};

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

@@ -0,0 +1,65 @@
+export 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)`);
+    }
+}

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

@@ -1,7 +1,6 @@
-import React from 'react';
 import type { LinearSyntenyViewModel } from '../model';
 type LSV = LinearSyntenyViewModel;
 declare const LinearSyntenyView: ({ model }: {
     model: LSV;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default LinearSyntenyView;