@jbrowse/plugin-dotplot-view 2.18.0 → 3.0.1

package/esm/DotplotView/components/ExportSvgDialog.js

@@ -1,15 +1,13 @@
-import React, { useState } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
 import { getSession, useLocalStorage } from '@jbrowse/core/util';
 import { Button, Checkbox, CircularProgress, DialogActions, DialogContent, FormControlLabel, MenuItem, TextField, Typography, } from '@mui/material';
 function LoadingMessage() {
-    return (React.createElement("div", null,
-        React.createElement(CircularProgress, { size: 20, style: { marginRight: 20 } }),
-        React.createElement(Typography, { display: "inline" }, "Creating SVG")));
+    return (_jsxs("div", { children: [_jsx(CircularProgress, { size: 20, style: { marginRight: 20 } }), _jsx(Typography, { display: "inline", children: "Creating SVG" })] }));
 }
 function TextField2({ children, ...rest }) {
-    return (React.createElement("div", null,
-        React.createElement(TextField, { ...rest }, children)));
+    return (_jsx("div", { children: _jsx(TextField, { ...rest, children: children }) }));
 }
 function useSvgLocal(key, val) {
     return useLocalStorage(`svg-${key}`, val);
@@ -22,39 +20,31 @@ export default function ExportSvgDialog({ model, handleClose, }) {
     const [error, setError] = useState();
     const [filename, setFilename] = useSvgLocal('file', 'jbrowse.svg');
     const [themeName, setThemeName] = useSvgLocal('theme', session.themeName || 'default');
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
-        React.createElement(DialogContent, null,
-            error ? (React.createElement(ErrorMessage, { error: error })) : loading ? (React.createElement(LoadingMessage, null)) : null,
-            React.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => {
-                    setFilename(event.target.value);
-                } }),
-            session.allThemes ? (React.createElement(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => {
-                    setThemeName(event.target.value);
-                } }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, val.name || '(Unknown name)'))))) : null,
-            offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => {
-                        setRasterizeLayers(val => !val);
-                    } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                    handleClose();
-                } }, "Cancel"),
-            React.createElement(Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
-                    setLoading(true);
-                    setError(undefined);
-                    try {
-                        await model.exportSvg({
-                            rasterizeLayers,
-                            filename,
-                            themeName,
-                        });
-                        handleClose();
-                    }
-                    catch (e) {
-                        console.error(e);
-                        setError(e);
-                    }
-                    finally {
-                        setLoading(false);
-                    }
-                } }, "Submit"))));
+    return (_jsxs(Dialog, { open: true, onClose: handleClose, title: "Export SVG", children: [_jsxs(DialogContent, { children: [error ? (_jsx(ErrorMessage, { error: error })) : loading ? (_jsx(LoadingMessage, {})) : null, _jsx(TextField2, { helperText: "filename", value: filename, onChange: event => {
+                            setFilename(event.target.value);
+                        } }), session.allThemes ? (_jsx(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => {
+                            setThemeName(event.target.value);
+                        }, children: Object.entries(session.allThemes()).map(([key, val]) => (_jsx(MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) })) : null, offscreenCanvas ? (_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: rasterizeLayers, onChange: () => {
+                                setRasterizeLayers(val => !val);
+                            } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (_jsx(Typography, { children: "Note: rasterizing layers not yet supported in this browser, so SVG size may be large" }))] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" }), _jsx(Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
+                            setLoading(true);
+                            setError(undefined);
+                            try {
+                                await model.exportSvg({
+                                    rasterizeLayers,
+                                    filename,
+                                    themeName,
+                                });
+                                handleClose();
+                            }
+                            catch (e) {
+                                console.error(e);
+                                setError(e);
+                            }
+                            finally {
+                                setLoading(false);
+                            }
+                        }, children: "Submit" })] })] }));
 }

package/esm/DotplotView/components/Grid.d.ts

@@ -1,10 +1,9 @@
-import React from 'react';
 import type { DotplotViewModel } from '../model';
 export declare const GridRaw: ({ model, children, }: {
     model: DotplotViewModel;
     children?: React.ReactNode;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default function Grid({ model, children, }: {
     model: DotplotViewModel;
     children?: React.ReactNode;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/DotplotView/components/Grid.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { getFillProps, getStrokeProps } from '@jbrowse/core/util';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -21,31 +21,23 @@ export const GridRaw = observer(function ({ model, children, }) {
     const h = Math.min(viewHeight - vbottom - ry, viewHeight);
     let lastx = Number.POSITIVE_INFINITY;
     let lasty = Number.POSITIVE_INFINITY;
-    return (React.createElement(React.Fragment, null,
-        React.createElement("rect", { x: rx, y: ry, width: w, height: h, ...getFillProps(theme.palette.background.default) }),
-        React.createElement("g", null,
-            hblocks.map(region => {
-                const x = region.offsetPx - hview.offsetPx;
-                const render = Math.floor(x) !== Math.floor(lastx);
-                if (render) {
-                    lastx = x;
-                }
-                return render ? (React.createElement("line", { key: JSON.stringify(region), x1: x, y1: 0, x2: x, y2: viewHeight, ...getStrokeProps(stroke) })) : null;
-            }),
-            vblocks.map(region => {
-                const y = viewHeight - (region.offsetPx - vview.offsetPx);
-                const render = Math.floor(y) !== Math.floor(lasty);
-                if (render) {
-                    lasty = y;
-                }
-                return render ? (React.createElement("line", { key: JSON.stringify(region), x1: 0, y1: y, x2: viewWidth, y2: y, ...getStrokeProps(stroke) })) : null;
-            }),
-            React.createElement("line", { x1: htop, y1: 0, x2: htop, y2: viewHeight, ...getStrokeProps(stroke) }),
-            React.createElement("line", { x1: 0, y1: viewHeight - vtop, x2: viewWidth, y2: viewHeight - vtop, ...getStrokeProps(stroke) })),
-        children));
+    return (_jsxs(_Fragment, { children: [_jsx("rect", { x: rx, y: ry, width: w, height: h, ...getFillProps(theme.palette.background.default) }), _jsxs("g", { children: [hblocks.map(region => {
+                        const x = region.offsetPx - hview.offsetPx;
+                        const render = Math.floor(x) !== Math.floor(lastx);
+                        if (render) {
+                            lastx = x;
+                        }
+                        return render ? (_jsx("line", { x1: x, y1: 0, x2: x, y2: viewHeight, ...getStrokeProps(stroke) }, JSON.stringify(region))) : null;
+                    }), vblocks.map(region => {
+                        const y = viewHeight - (region.offsetPx - vview.offsetPx);
+                        const render = Math.floor(y) !== Math.floor(lasty);
+                        if (render) {
+                            lasty = y;
+                        }
+                        return render ? (_jsx("line", { x1: 0, y1: y, x2: viewWidth, y2: y, ...getStrokeProps(stroke) }, JSON.stringify(region))) : null;
+                    }), _jsx("line", { x1: htop, y1: 0, x2: htop, y2: viewHeight, ...getStrokeProps(stroke) }), _jsx("line", { x1: 0, y1: viewHeight - vtop, x2: viewWidth, y2: viewHeight - vtop, ...getStrokeProps(stroke) })] }), children] }));
 });
 export default function Grid({ model, children, }) {
     const { viewWidth, viewHeight } = model;
-    return (React.createElement("svg", { width: viewWidth, height: viewHeight, style: { background: 'rgba(0,0,0,0.12)' } },
-        React.createElement(GridRaw, { model: model }, children)));
+    return (_jsx("svg", { width: viewWidth, height: viewHeight, style: { background: 'rgba(0,0,0,0.12)' }, children: _jsx(GridRaw, { model: model, children: children }) }));
 }

package/esm/DotplotView/components/Header.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { DotplotViewModel } from '../model';
 declare const DotplotHeader: ({ model, selection, }: {
     model: DotplotViewModel;
@@ -6,5 +5,5 @@ declare const DotplotHeader: ({ model, selection, }: {
         width: number;
         height: number;
     };
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default DotplotHeader;

package/esm/DotplotView/components/Header.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getBpDisplayStr } from '@jbrowse/core/util';
 import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -23,25 +23,6 @@ const useStyles = makeStyles()({
 const DotplotHeader = observer(function ({ model, selection, }) {
     const { classes } = useStyles();
     const { hview, vview, showPanButtons } = model;
-    return (React.createElement("div", { className: classes.headerBar },
-        React.createElement(DotplotControls, { model: model }),
-        React.createElement(Typography, { className: classes.bp, variant: "body2", color: "textSecondary" },
-            "x: ",
-            hview.assemblyNames.join(','),
-            " ",
-            getBpDisplayStr(hview.currBp),
-            React.createElement("br", null),
-            "y: ",
-            vview.assemblyNames.join(','),
-            " ",
-            getBpDisplayStr(vview.currBp)),
-        selection ? (React.createElement(Typography, { className: classes.bp, variant: "body2", color: "textSecondary" },
-            `width:${getBpDisplayStr(hview.bpPerPx * selection.width)}`,
-            " ",
-            React.createElement("br", null),
-            `height:${getBpDisplayStr(vview.bpPerPx * selection.height)}`)) : null,
-        React.createElement("div", { className: classes.spacer }),
-        React.createElement(DotplotWarnings, { model: model }),
-        showPanButtons ? React.createElement(PanButtons, { model: model }) : null));
+    return (_jsxs("div", { className: classes.headerBar, children: [_jsx(DotplotControls, { model: model }), _jsxs(Typography, { className: classes.bp, variant: "body2", color: "textSecondary", children: ["x: ", hview.assemblyNames.join(','), " ", getBpDisplayStr(hview.currBp), _jsx("br", {}), "y: ", vview.assemblyNames.join(','), " ", getBpDisplayStr(vview.currBp)] }), selection ? (_jsxs(Typography, { className: classes.bp, variant: "body2", color: "textSecondary", children: [`width:${getBpDisplayStr(hview.bpPerPx * selection.width)}`, " ", _jsx("br", {}), `height:${getBpDisplayStr(vview.bpPerPx * selection.height)}`] })) : null, _jsx("div", { className: classes.spacer }), _jsx(DotplotWarnings, { model: model }), showPanButtons ? _jsx(PanButtons, { model: model }) : null] }));
 });
 export default DotplotHeader;

package/esm/DotplotView/components/ImportForm/ImportSyntenyOpenCustomTrack.d.ts

@@ -0,0 +1,7 @@
+import type { DotplotViewModel } from '../../model';
+declare const ImportSyntenyOpenCustomTrack: ({ model, assembly1, assembly2, }: {
+    model: DotplotViewModel;
+    assembly1: string;
+    assembly2: string;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ImportSyntenyOpenCustomTrack;

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

@@ -0,0 +1,124 @@
+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, }) {
+    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(0, {
+                    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,
+        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/DotplotView/components/ImportForm/ImportSyntenyTrackSelector.d.ts

@@ -1,9 +1,7 @@
-import React from 'react';
 import type { DotplotViewModel } from '../../model';
-declare const Selector: ({ model, assembly1, assembly2, setShowTrackId, }: {
+declare const ImportSyntenyTrackSelector: ({ model, assembly1, assembly2, }: {
     model: DotplotViewModel;
     assembly1: string;
     assembly2: string;
-    setShowTrackId: (arg: string) => void;
-}) => React.JSX.Element;
-export default Selector;
+}) => import("react/jsx-runtime").JSX.Element;
+export default ImportSyntenyTrackSelector;

package/esm/DotplotView/components/ImportForm/ImportSyntenyTrackSelector.js

@@ -1,4 +1,5 @@
-import React, { useEffect, useState } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
@@ -12,7 +13,7 @@ function f(track, assembly1, assembly2) {
         assemblyNames.includes(assembly2) &&
         track.type.includes('Synteny'));
 }
-const Selector = observer(({ model, assembly1, assembly2, setShowTrackId, }) => {
+const ImportSyntenyTrackSelector = observer(function ({ model, assembly1, assembly2, }) {
     var _a;
     const session = getSession(model);
     const { tracks, sessionTracks } = session;
@@ -27,17 +28,13 @@ const Selector = observer(({ model, assembly1, assembly2, setShowTrackId, }) =>
         setValue(resetTrack);
     }, [resetTrack]);
     useEffect(() => {
-        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\"."),
-        React.createElement(Typography, { paragraph: true },
-            "Note: there is a track selector ",
-            React.createElement("i", null, "inside"),
-            " the DotplotView, which can turn on one or more SyntenyTracks (more than one can be displayed at once). Look for the track selector icon ",
-            React.createElement(TrackSelectorIcon, null)),
-        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}` }))));
+        model.setImportFormSyntenyTrack(0, {
+            type: 'preConfigured',
+            value,
+        });
+    }, [model, value]);
+    return (_jsxs(Paper, { style: { padding: 12 }, children: [_jsxs(Typography, { children: ["Select a track from the select box below, the track will be shown when you hit \"Launch\". Note: there is a track selector ", _jsx("i", { children: "inside" }), " the DotplotView, which can turn on one or more SyntenyTracks (more than one can be displayed at once). Look for the track selector icon", ' ', _jsx(TrackSelectorIcon, {})] }), filteredTracks.length ? (_jsx(Select, { value: value, onChange: event => {
+                    setValue(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 Selector;
+export default ImportSyntenyTrackSelector;

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

@@ -0,0 +1,7 @@
+import type { DotplotViewModel } from '../../model';
+declare const TrackSelector: ({ assembly1, assembly2, model, }: {
+    model: DotplotViewModel;
+    assembly1: string;
+    assembly2: string;
+}) => import("react/jsx-runtime").JSX.Element;
+export default TrackSelector;

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

@@ -0,0 +1,18 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { FormControl, FormControlLabel, FormLabel, Radio, RadioGroup, } from '@mui/material';
+import { observer } from 'mobx-react';
+import ImportSyntenyOpenCustomTrack from './ImportSyntenyOpenCustomTrack';
+import ImportSyntenyTrackSelector from './ImportSyntenyTrackSelector';
+const TrackSelector = observer(function ({ assembly1, assembly2, model, }) {
+    const [choice, setChoice] = useState('tracklist');
+    useEffect(() => {
+        if (choice === 'none') {
+            model.setImportFormSyntenyTrack(0, { type: 'none' });
+        }
+    }, [model, choice]);
+    return (_jsxs(_Fragment, { children: [_jsxs(FormControl, { children: [_jsx(FormLabel, { id: "group-label", children: "(Optional) Select or add a synteny track" }), _jsxs(RadioGroup, { row: true, value: choice, onChange: event => {
+                            setChoice(event.target.value);
+                        }, "aria-labelledby": "group-label", 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(ImportSyntenyOpenCustomTrack, { model: model, assembly2: assembly2, assembly1: assembly1 })) : null, choice === 'tracklist' ? (_jsx(ImportSyntenyTrackSelector, { model: model, assembly1: assembly1, assembly2: assembly2 })) : null] }));
+});
+export default TrackSelector;

package/esm/DotplotView/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/DotplotView/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/DotplotView/components/ImportForm/index.d.ts

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