@jbrowse/plugin-dotplot-view 2.6.1

package/esm/DotplotView/components/ExportSvgDialog.js

@@ -0,0 +1,50 @@
+import React, { useState } from 'react';
+import { Button, Checkbox, CircularProgress, DialogActions, DialogContent, FormControlLabel, MenuItem, TextField, Typography, } from '@mui/material';
+import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
+import { getSession, useLocalStorage } from '@jbrowse/core/util';
+function LoadingMessage() {
+    return (React.createElement("div", null,
+        React.createElement(CircularProgress, { size: 20, style: { marginRight: 20 } }),
+        React.createElement(Typography, { display: "inline" }, "Creating SVG")));
+}
+function useSvgLocal(key, val) {
+    return useLocalStorage('svg-' + key, val);
+}
+export default function ExportSvgDlg({ model, handleClose, }) {
+    const session = getSession(model);
+    const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
+    const [rasterizeLayers, setRasterizeLayers] = useState(offscreenCanvas);
+    const [loading, setLoading] = useState(false);
+    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(TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            React.createElement("br", null),
+            session.allThemes ? (React.createElement(TextField, { 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 }, 
+            // @ts-expect-error
+            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);
+                        setLoading(false);
+                    }
+                } }, "Submit"))));
+}
+//# sourceMappingURL=ExportSvgDialog.js.map

package/esm/DotplotView/components/ExportSvgDialog.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ExportSvgDialog.js","sourceRoot":"","sources":["../../../src/DotplotView/components/ExportSvgDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,gBAAgB,EAChB,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,QAAQ,EACR,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAEvD,OAAO,EAAE,UAAU,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AAEhE,SAAS,cAAc;IACrB,OAAO,CACL;QACE,oBAAC,gBAAgB,IAAC,IAAI,EAAE,EAAE,EAAE,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,GAAI;QAC1D,oBAAC,UAAU,IAAC,OAAO,EAAC,QAAQ,mBAA0B,CAClD,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAI,GAAW,EAAE,GAAM;IACzC,OAAO,eAAe,CAAC,MAAM,GAAG,GAAG,EAAE,GAAG,CAAC,CAAA;AAC3C,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,EACnC,KAAK,EACL,WAAW,GAIZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,eAAe,GAAG,OAAO,eAAe,KAAK,WAAW,CAAA;IAC9D,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,CAAC,eAAe,CAAC,CAAA;IACvE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,WAAW,CAAC,MAAM,EAAE,aAAa,CAAC,CAAA;IAClE,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,WAAW,CAC3C,OAAO,EACP,OAAO,CAAC,SAAS,IAAI,SAAS,CAC/B,CAAA;IACD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,YAAY;QACnD,oBAAC,aAAa;YACX,KAAK,CAAC,CAAC,CAAC,CACP,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CACZ,oBAAC,cAAc,OAAG,CACnB,CAAC,CAAC,CAAC,IAAI;YACR,oBAAC,SAAS,IACR,UAAU,EAAC,UAAU,EACrB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAClD;YACF,+BAAM;YACL,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,CACnB,oBAAC,SAAS,IACR,MAAM,QACN,KAAK,EAAC,OAAO,EACb,KAAK,EAAE,SAAS,EAChB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,IAElD,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CACvD,oBAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG;YAE1B,mBAAmB;YACnB,GAAG,CAAC,IAAI,IAAI,gBAAgB,CAErB,CACZ,CAAC,CACQ,CACb,CAAC,CAAC,CAAC,IAAI;YACP,eAAe,CAAC,CAAC,CAAC,CACjB,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,eAAe,EACxB,QAAQ,EAAE,GAAG,EAAE,CAAC,kBAAkB,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC/C,EAEJ,KAAK,EAAC,8EAA8E,GACpF,CACH,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,+FAGE,CACd,CACa;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,KAAK,IAAI,EAAE;oBAClB,UAAU,CAAC,IAAI,CAAC,CAAA;oBAChB,QAAQ,CAAC,SAAS,CAAC,CAAA;oBACnB,IAAI;wBACF,MAAM,KAAK,CAAC,SAAS,CAAC;4BACpB,eAAe;4BACf,QAAQ;4BACR,SAAS;yBACV,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;qBACd;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACX,UAAU,CAAC,KAAK,CAAC,CAAA;qBAClB;gBACH,CAAC,aAGM,CACK,CACT,CACV,CAAA;AACH,CAAC"}

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

@@ -0,0 +1,10 @@
+import React from 'react';
+import { DotplotViewModel } from '../model';
+export declare const GridRaw: ({ model, children, }: {
+    model: DotplotViewModel;
+    children?: React.ReactNode;
+}) => React.JSX.Element | null;
+export default function Grid({ model, children, }: {
+    model: DotplotViewModel;
+    children?: React.ReactNode;
+}): React.JSX.Element;

package/esm/DotplotView/components/Grid.js

@@ -0,0 +1,53 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { useTheme } from '@mui/material';
+export const GridRaw = observer(function ({ model, children, }) {
+    const { viewWidth, viewHeight, hview, vview } = model;
+    const hblocks = hview.dynamicBlocks.contentBlocks;
+    const vblocks = vview.dynamicBlocks.contentBlocks;
+    if (!hblocks.length || !vblocks.length) {
+        return null;
+    }
+    const htop = hview.displayedRegionsTotalPx - hview.offsetPx;
+    const vtop = vview.displayedRegionsTotalPx - vview.offsetPx;
+    const hbottom = hblocks[0].offsetPx - hview.offsetPx;
+    const vbottom = vblocks[0].offsetPx - vview.offsetPx;
+    const theme = useTheme();
+    const stroke = theme.palette.divider;
+    // Uses math.max/min avoid making very large SVG rect offscreen element,
+    // which can sometimes fail to draw
+    const rx = Math.max(hbottom, 0);
+    const ry = Math.max(viewHeight - vtop, 0);
+    const w = Math.min(htop - hbottom, viewWidth);
+    const h = Math.min(viewHeight - vbottom - ry, viewHeight);
+    let lastx = Infinity;
+    let lasty = Infinity;
+    return (React.createElement(React.Fragment, null,
+        React.createElement("rect", { x: rx, y: ry, width: w, height: h, fill: 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, stroke: 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, stroke: stroke })) : null;
+            }),
+            React.createElement("line", { x1: htop, y1: 0, x2: htop, y2: viewHeight, stroke: stroke }),
+            React.createElement("line", { x1: 0, y1: viewHeight - vtop, x2: viewWidth, y2: viewHeight - vtop, stroke: 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)));
+}
+//# sourceMappingURL=Grid.js.map

package/esm/DotplotView/components/Grid.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Grid.js","sourceRoot":"","sources":["../../../src/DotplotView/components/Grid.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAKxC,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACrD,MAAM,OAAO,GAAG,KAAK,CAAC,aAAa,CAAC,aAAa,CAAA;IACjD,MAAM,OAAO,GAAG,KAAK,CAAC,aAAa,CAAC,aAAa,CAAA;IACjD,IAAI,CAAC,OAAO,CAAC,MAAM,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE;QACtC,OAAO,IAAI,CAAA;KACZ;IACD,MAAM,IAAI,GAAG,KAAK,CAAC,uBAAuB,GAAG,KAAK,CAAC,QAAQ,CAAA;IAC3D,MAAM,IAAI,GAAG,KAAK,CAAC,uBAAuB,GAAG,KAAK,CAAC,QAAQ,CAAA;IAC3D,MAAM,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAA;IACpD,MAAM,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAA;IACpD,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,OAAO,CAAA;IAEpC,wEAAwE;IACxE,mCAAmC;IACnC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;IAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,GAAG,IAAI,EAAE,CAAC,CAAC,CAAA;IACzC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,OAAO,EAAE,SAAS,CAAC,CAAA;IAC7C,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,GAAG,OAAO,GAAG,EAAE,EAAE,UAAU,CAAC,CAAA;IAEzD,IAAI,KAAK,GAAG,QAAQ,CAAA;IACpB,IAAI,KAAK,GAAG,QAAQ,CAAA;IACpB,OAAO,CACL;QACE,8BACE,CAAC,EAAE,EAAE,EACL,CAAC,EAAE,EAAE,EACL,KAAK,EAAE,CAAC,EACR,MAAM,EAAE,CAAC,EACT,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,GACtC;QACF;YACG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBACpB,MAAM,CAAC,GAAG,MAAM,CAAC,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAA;gBAC1C,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBAClD,IAAI,MAAM,EAAE;oBACV,KAAK,GAAG,CAAC,CAAA;iBACV;gBACD,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,8BACE,GAAG,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,EAC3B,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,UAAU,EACd,MAAM,EAAE,MAAM,GACd,CACH,CAAC,CAAC,CAAC,IAAI,CAAA;YACV,CAAC,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBACpB,MAAM,CAAC,GAAG,UAAU,GAAG,CAAC,MAAM,CAAC,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAA;gBACzD,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBAClD,IAAI,MAAM,EAAE;oBACV,KAAK,GAAG,CAAC,CAAA;iBACV;gBACD,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,8BACE,GAAG,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,EAC3B,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,SAAS,EACb,EAAE,EAAE,CAAC,EACL,MAAM,EAAE,MAAM,GACd,CACH,CAAC,CAAC,CAAC,IAAI,CAAA;YACV,CAAC,CAAC;YACF,8BAAM,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,UAAU,EAAE,MAAM,EAAE,MAAM,GAAI;YACnE,8BACE,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,UAAU,GAAG,IAAI,EACrB,EAAE,EAAE,SAAS,EACb,EAAE,EAAE,UAAU,GAAG,IAAI,EACrB,MAAM,EAAE,MAAM,GACd,CACA;QACH,QAAQ,CACR,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,IAAI,CAAC,EAC3B,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IACvC,OAAO,CACL,6BACE,KAAK,EAAE,SAAS,EAChB,MAAM,EAAE,UAAU,EAClB,KAAK,EAAE,EAAE,UAAU,EAAE,kBAAkB,EAAE;QAEzC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,IAAG,QAAQ,CAAW,CACvC,CACP,CAAA;AACH,CAAC"}

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

@@ -0,0 +1,10 @@
+import React from 'react';
+import { DotplotViewModel } from '../model';
+declare const _default: ({ model, selection, }: {
+    model: DotplotViewModel;
+    selection?: {
+        width: number;
+        height: number;
+    } | undefined;
+}) => React.JSX.Element;
+export default _default;

package/esm/DotplotView/components/Header.js

@@ -0,0 +1,140 @@
+import React, { useState } from 'react';
+import { IconButton, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { getBpDisplayStr } from '@jbrowse/core/util';
+import { Menu } from '@jbrowse/core/ui';
+// icons
+import ZoomOut from '@mui/icons-material/ZoomOut';
+import ZoomIn from '@mui/icons-material/ZoomIn';
+import MoreVert from '@mui/icons-material/MoreVert';
+import { CursorMouse, CursorMove } from './CursorIcon';
+import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
+import DotplotWarnings from './DotplotWarnings';
+import PanButtons from './PanButtons';
+const useStyles = makeStyles()({
+    iconButton: {
+        margin: 5,
+    },
+    bp: {
+        display: 'flex',
+        alignItems: 'center',
+        marginLeft: 10,
+    },
+    spacer: {
+        flexGrow: 1,
+    },
+    headerBar: {
+        display: 'flex',
+        position: 'relative',
+    },
+});
+const DotplotControls = observer(({ model }) => {
+    const { classes } = useStyles();
+    const [menuAnchorEl, setMenuAnchorEl] = useState();
+    return (React.createElement("div", null,
+        React.createElement(IconButton, { onClick: model.zoomOutButton, className: classes.iconButton },
+            React.createElement(ZoomOut, null)),
+        React.createElement(IconButton, { onClick: model.zoomInButton, className: classes.iconButton },
+            React.createElement(ZoomIn, null)),
+        React.createElement(IconButton, { onClick: () => model.activateTrackSelector(), className: classes.iconButton, title: "Open track selector", "data-testid": "circular_track_select" },
+            React.createElement(TrackSelectorIcon, null)),
+        React.createElement(IconButton, { onClick: event => setMenuAnchorEl(event.currentTarget), className: classes.iconButton },
+            React.createElement(MoreVert, null)),
+        menuAnchorEl ? (React.createElement(Menu, { anchorEl: menuAnchorEl, open: true, onMenuItemClick: (_event, callback) => {
+                callback();
+                setMenuAnchorEl(undefined);
+            }, menuItems: [
+                {
+                    onClick: () => model.squareView(),
+                    label: 'Square view - same base pairs per pixel',
+                },
+                {
+                    onClick: () => model.squareViewProportional(),
+                    label: 'Rectanglularize view - same total bp',
+                },
+                {
+                    onClick: () => model.showAllRegions(),
+                    label: 'Show all regions',
+                },
+                {
+                    onClick: () => model.setDrawCigar(!model.drawCigar),
+                    type: 'checkbox',
+                    label: 'Draw CIGAR',
+                    checked: model.drawCigar,
+                },
+                {
+                    onClick: () => model.setShowPanButtons(!model.showPanButtons),
+                    label: 'Show pan buttons',
+                    type: 'checkbox',
+                    checked: model.showPanButtons,
+                },
+                {
+                    label: 'Click and drag mode',
+                    subMenu: [
+                        {
+                            onClick: () => model.setCursorMode('move'),
+                            label: 'Pan by default, select region when ctrl key is held',
+                            icon: CursorMove,
+                            type: 'radio',
+                            checked: model.cursorMode === 'move',
+                        },
+                        {
+                            onClick: () => model.setCursorMode('crosshair'),
+                            label: 'Select region by default, pan when ctrl key is held',
+                            icon: CursorMouse,
+                            type: 'radio',
+                            checked: model.cursorMode === 'crosshair',
+                        },
+                    ],
+                },
+                {
+                    label: 'Wheel scroll mode',
+                    subMenu: [
+                        {
+                            onClick: () => model.setWheelMode('pan'),
+                            label: 'Pans view',
+                            type: 'radio',
+                            checked: model.wheelMode === 'pan',
+                        },
+                        {
+                            onClick: () => model.setWheelMode('zoom'),
+                            label: 'Zooms view',
+                            type: 'radio',
+                            checked: model.wheelMode === 'zoom',
+                        },
+                        {
+                            onClick: () => model.setWheelMode('none'),
+                            label: 'Disable',
+                            type: 'radio',
+                            checked: model.wheelMode === 'none',
+                        },
+                    ],
+                },
+            ], onClose: () => setMenuAnchorEl(undefined) })) : null));
+});
+export default observer(function Header({ 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));
+});
+//# sourceMappingURL=Header.js.map

package/esm/DotplotView/components/Header.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/DotplotView/components/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAA;AAEvC,QAAQ;AACR,OAAO,OAAO,MAAM,6BAA6B,CAAA;AACjD,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACtD,OAAO,EAAE,aAAa,IAAI,iBAAiB,EAAE,MAAM,wBAAwB,CAAA;AAI3E,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;KACV;IACD,EAAE,EAAE;QACF,OAAO,EAAE,MAAM;QACf,UAAU,EAAE,QAAQ;QACpB,UAAU,EAAE,EAAE;KACf;IACD,MAAM,EAAE;QACN,QAAQ,EAAE,CAAC;KACZ;IACD,SAAS,EAAE;QACT,OAAO,EAAE,MAAM;QACf,QAAQ,EAAE,UAAU;KACrB;CACF,CAAC,CAAA;AAEF,MAAM,eAAe,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA+B,EAAE,EAAE;IAC1E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,EAAe,CAAA;IAC/D,OAAO,CACL;QACE,oBAAC,UAAU,IAAC,OAAO,EAAE,KAAK,CAAC,aAAa,EAAE,SAAS,EAAE,OAAO,CAAC,UAAU;YACrE,oBAAC,OAAO,OAAG,CACA;QAEb,oBAAC,UAAU,IAAC,OAAO,EAAE,KAAK,CAAC,YAAY,EAAE,SAAS,EAAE,OAAO,CAAC,UAAU;YACpE,oBAAC,MAAM,OAAG,CACC;QAEb,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAC5C,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,KAAK,EAAC,qBAAqB,iBACf,uBAAuB;YAEnC,oBAAC,iBAAiB,OAAG,CACV;QAEb,oBAAC,UAAU,IACT,OAAO,EAAE,KAAK,CAAC,EAAE,CAAC,eAAe,CAAC,KAAK,CAAC,aAAa,CAAC,EACtD,SAAS,EAAE,OAAO,CAAC,UAAU;YAE7B,oBAAC,QAAQ,OAAG,CACD;QAEZ,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,IAAI,IACH,QAAQ,EAAE,YAAY,EACtB,IAAI,QACJ,eAAe,EAAE,CAAC,MAAM,EAAE,QAAQ,EAAE,EAAE;gBACpC,QAAQ,EAAE,CAAA;gBACV,eAAe,CAAC,SAAS,CAAC,CAAA;YAC5B,CAAC,EACD,SAAS,EAAE;gBACT;oBACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,UAAU,EAAE;oBACjC,KAAK,EAAE,yCAAyC;iBACjD;gBACD;oBACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,sBAAsB,EAAE;oBAC7C,KAAK,EAAE,sCAAsC;iBAC9C;gBACD;oBACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,cAAc,EAAE;oBACrC,KAAK,EAAE,kBAAkB;iBAC1B;gBACD;oBACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,KAAK,CAAC,SAAS,CAAC;oBACnD,IAAI,EAAE,UAAU;oBAChB,KAAK,EAAE,YAAY;oBACnB,OAAO,EAAE,KAAK,CAAC,SAAS;iBACzB;gBACD;oBACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,CAAC,KAAK,CAAC,cAAc,CAAC;oBAC7D,KAAK,EAAE,kBAAkB;oBACzB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,KAAK,CAAC,cAAc;iBAC9B;gBACD;oBACE,KAAK,EAAE,qBAAqB;oBAC5B,OAAO,EAAE;wBACP;4BACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,MAAM,CAAC;4BAC1C,KAAK,EAAE,qDAAqD;4BAC5D,IAAI,EAAE,UAAU;4BAChB,IAAI,EAAE,OAAO;4BACb,OAAO,EAAE,KAAK,CAAC,UAAU,KAAK,MAAM;yBACrC;wBACD;4BACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,WAAW,CAAC;4BAC/C,KAAK,EAAE,qDAAqD;4BAC5D,IAAI,EAAE,WAAW;4BACjB,IAAI,EAAE,OAAO;4BACb,OAAO,EAAE,KAAK,CAAC,UAAU,KAAK,WAAW;yBAC1C;qBACF;iBACF;gBACD;oBACE,KAAK,EAAE,mBAAmB;oBAC1B,OAAO,EAAE;wBACP;4BACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,KAAK,CAAC;4BACxC,KAAK,EAAE,WAAW;4BAClB,IAAI,EAAE,OAAO;4BACb,OAAO,EAAE,KAAK,CAAC,SAAS,KAAK,KAAK;yBACnC;wBACD;4BACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC;4BACzC,KAAK,EAAE,YAAY;4BACnB,IAAI,EAAE,OAAO;4BACb,OAAO,EAAE,KAAK,CAAC,SAAS,KAAK,MAAM;yBACpC;wBACD;4BACE,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC;4BACzC,KAAK,EAAE,SAAS;4BAChB,IAAI,EAAE,OAAO;4BACb,OAAO,EAAE,KAAK,CAAC,SAAS,KAAK,MAAM;yBACpC;qBACF;iBACF;aACF,EACD,OAAO,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,SAAS,CAAC,GACzC,CACH,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAC,SAAS,MAAM,CAAC,EACtC,KAAK,EACL,SAAS,GAIV;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAC9C,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS;QAC/B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,EAAE,EAAE,OAAO,EAAC,OAAO,EAAC,KAAK,EAAC,eAAe;;YAClE,KAAK,CAAC,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC;;YAAG,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC;YACjE,+BAAM;;YACF,KAAK,CAAC,aAAa,CAAC,IAAI,CAAC,GAAG,CAAC;;YAAG,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,CACtD;QACZ,SAAS,CAAC,CAAC,CAAC,CACX,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,EAAE,EACrB,OAAO,EAAC,OAAO,EACf,KAAK,EAAC,eAAe;YAEpB,SAAS,eAAe,CAAC,KAAK,CAAC,OAAO,GAAG,SAAS,CAAC,KAAK,CAAC,EAAE;;YAAE,+BAAM;YACnE,UAAU,eAAe,CAAC,KAAK,CAAC,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,EAAE,CACnD,CACd,CAAC,CAAC,CAAC,IAAI;QACR,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM,GAAI;QAClC,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,cAAc,CAAC,CAAC,CAAC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CACjD,CACP,CAAA;AACH,CAAC,CAAC,CAAA"}

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

@@ -0,0 +1,11 @@
+import React from 'react';
+import { SnapshotIn } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+type Conf = SnapshotIn<AnyConfigurationModel>;
+declare const OpenTrack: ({ sessionTrackData, assembly1, assembly2, setSessionTrackData, }: {
+    sessionTrackData: Conf;
+    assembly1: string;
+    assembly2: string;
+    setSessionTrackData: (arg: Conf) => void;
+}) => React.JSX.Element;
+export default OpenTrack;

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

@@ -0,0 +1 @@
+{"version":3,"file":"ImportCustomTrack.js","sourceRoot":"","sources":["../../../src/DotplotView/components/ImportCustomTrack.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EACL,gBAAgB,EAChB,IAAI,EACJ,KAAK,EACL,KAAK,EACL,UAAU,EACV,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAE7D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,SAAS,OAAO,CACd,gBAA6E;IAE7E,OAAO,gBAAgB;QACrB,CAAC,CAAC,mBAAmB;YACnB,gBAAgB,CAAC,GAAG;gBAClB,mBAAmB;gBACnB,gBAAgB,CAAC,SAAS;gBAC1B,mBAAmB;gBACnB,gBAAgB,CAAC,IAAI;QACzB,CAAC,CAAC,SAAS,CAAA;AACf,CAAC;AAED,SAAS,OAAO,CAAC,QAAgB;IAC/B,OAAO,QAAQ,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAA;AACpE,CAAC;AAED,SAAS,UAAU,CAAC,EAClB,WAAW,EACX,SAAS,EACT,SAAS,EACT,YAAY,EACZ,YAAY,EACZ,YAAY,GAQb;IACC,IAAI,WAAW,KAAK,MAAM,EAAE;QAC1B,OAAO;YACL,IAAI,EAAE,YAAY;YAClB,WAAW,EAAE,YAAY;YACzB,aAAa,EAAE,SAAS;YACxB,cAAc,EAAE,SAAS;SAC1B,CAAA;KACF;SAAM,IAAI,WAAW,KAAK,MAAM,EAAE;QACjC,OAAO;YACL,IAAI,EAAE,gBAAgB;YACtB,WAAW,EAAE,YAAY;YACzB,aAAa,EAAE,SAAS;YACxB,cAAc,EAAE,SAAS;SAC1B,CAAA;KACF;SAAM,IAAI,WAAW,KAAK,QAAQ,EAAE;QACnC,OAAO;YACL,IAAI,EAAE,cAAc;YACpB,aAAa,EAAE,YAAY;YAC3B,aAAa,EAAE,SAAS;YACxB,cAAc,EAAE,SAAS;SAC1B,CAAA;KACF;SAAM,IAAI,WAAW,KAAK,QAAQ,EAAE;QACnC,OAAO;YACL,IAAI,EAAE,cAAc;YACpB,aAAa,EAAE,YAAY;YAC3B,aAAa,EAAE,SAAS;YACxB,cAAc,EAAE,SAAS;SAC1B,CAAA;KACF;SAAM,IAAI,WAAW,KAAK,UAAU,EAAE;QACrC,OAAO;YACL,IAAI,EAAE,sBAAsB;YAC5B,qBAAqB,EAAE,YAAY;YACnC,YAAY;YACZ,YAAY;YACZ,aAAa,EAAE,CAAC,SAAS,EAAE,SAAS,CAAC;SACtC,CAAA;KACF;SAAM,IAAI,WAAW,KAAK,iBAAiB,EAAE;QAC5C,OAAO;YACL,IAAI,EAAE,4BAA4B;YAClC,2BAA2B,EAAE,YAAY;YACzC,YAAY;YACZ,YAAY;YACZ,aAAa,EAAE,CAAC,SAAS,EAAE,SAAS,CAAC;SACtC,CAAA;KACF;SAAM;QACL,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;KAChC;AACH,CAAC;AAID,MAAM,SAAS,GAAG,QAAQ,CACxB,CAAC,EACC,gBAAgB,EAChB,SAAS,EACT,SAAS,EACT,mBAAmB,GAMpB,EAAE,EAAE;IACH,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAChE,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAChE,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAChE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACtC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,QAAQ,GAAG,OAAO,CAAC,YAAY,CAAC,CAAA;IAEtC,MAAM,WAAW,GACf,KAAK,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;IAE5D,SAAS,CAAC,GAAG,EAAE;QACb,IAAI;YACF,IAAI,YAAY,EAAE;gBAChB,MAAM,EAAE,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;gBACzD,MAAM,OAAO,GAAG,GAAG,EAAE,IAAI,IAAI,CAAC,GAAG,EAAE,EAAE,CAAA;gBACrC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBAEnB,mBAAmB,CAAC;oBAClB,OAAO;oBACP,IAAI,EAAE,EAAE;oBACR,aAAa,EAAE,CAAC,SAAS,EAAE,SAAS,CAAC;oBACrC,IAAI,EAAE,cAAc;oBACpB,OAAO,EAAE,UAAU,CAAC;wBAClB,WAAW;wBACX,SAAS;wBACT,SAAS;wBACT,YAAY;wBACZ,YAAY;wBACZ,YAAY;qBACb,CAAC;iBACH,CAAC,CAAA;aACH;SACF;QAAC,OAAO,CAAC,EAAE;YACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;SACZ;IACH,CAAC,EAAE;QACD,QAAQ;QACR,SAAS;QACT,SAAS;QACT,YAAY;QACZ,YAAY;QACZ,YAAY;QACZ,WAAW;QACX,mBAAmB;KACpB,CAAC,CAAA;IACF,OAAO,CACL,oBAAC,KAAK,IAAC,KAAK,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;QAC1B,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,sUAM7B;QACb,oBAAC,UAAU,IACT,KAAK,EAAE,WAAW,EAClB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC;YAE/C,oBAAC,IAAI,IAAC,SAAS,QAAC,cAAc,EAAC,QAAQ;gBACrC,oBAAC,IAAI,IAAC,IAAI;oBACR,oBAAC,gBAAgB,IAAC,KAAK,EAAC,MAAM,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,MAAM,GAAG,CAC7D;gBACP,oBAAC,IAAI,IAAC,IAAI;oBACR,oBAAC,gBAAgB,IAAC,KAAK,EAAC,MAAM,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,MAAM,GAAG,CAC7D;gBACP,oBAAC,IAAI,IAAC,IAAI;oBACR,oBAAC,gBAAgB,IACf,KAAK,EAAC,QAAQ,EACd,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,QAAQ,GACd,CACG;gBACP,oBAAC,IAAI,IAAC,IAAI;oBACR,oBAAC,gBAAgB,IACf,KAAK,EAAC,QAAQ,EACd,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,QAAQ,GACd,CACG;gBACP,oBAAC,IAAI,IAAC,IAAI;oBACR,oBAAC,gBAAgB,IACf,KAAK,EAAC,UAAU,EAChB,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,UAAU,GAChB,CACG;gBACP,oBAAC,IAAI,IAAC,IAAI;oBACR,oBAAC,gBAAgB,IACf,KAAK,EAAC,iBAAiB,EACvB,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,iBAAiB,GACvB,CACG,CACF,CACI;QACb,oBAAC,IAAI,IAAC,SAAS,QAAC,cAAc,EAAC,QAAQ;YACrC,oBAAC,IAAI,IAAC,IAAI,UACP,KAAK,KAAK,UAAU,IAAI,KAAK,KAAK,iBAAiB,CAAC,CAAC,CAAC,CACrD;gBACE,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;;oBACd,KAAK;;oBAC2B,GAAG;oBAC7C,2BAAG,IAAI,EAAC,iEAAiE,kBAErE,CACA;gBACN,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,oBAAC,YAAY,IACX,IAAI,EAAC,eAAe,EACpB,WAAW,EAAC,EAAE,EACd,QAAQ,EAAE,YAAY,EACtB,WAAW,EAAE,GAAG,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,GACxC,CACE;oBACN;wBACE,oBAAC,YAAY,IACX,IAAI,EAAC,6CAA6C,EAClD,WAAW,EAAC,EAAE,EACd,QAAQ,EAAE,YAAY,EACtB,WAAW,EAAE,GAAG,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,GACxC,CACE;oBACN;wBACE,oBAAC,YAAY,IACX,IAAI,EAAC,8CAA8C,EACnD,WAAW,EAAC,EAAE,EACd,QAAQ,EAAE,YAAY,EACtB,WAAW,EAAE,GAAG,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,GACxC,CACE,CACF,CACF,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,YAAY,IACX,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,EACtC,WAAW,EAAC,EAAE,EACd,QAAQ,EAAE,YAAY,EACtB,WAAW,EAAE,GAAG,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,GACxC,CACH,CACI,CACF,CACD,CACT,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,SAAS,CAAA"}

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

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

package/esm/DotplotView/components/ImportForm.js

@@ -0,0 +1,93 @@
+import React, { useState, useEffect } from 'react';
+import { Button, Container, FormControl, FormLabel, FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { transaction } from 'mobx';
+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));
+}
+const DotplotImportForm = observer(({ 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();
+    function onOpenClick() {
+        try {
+            if (!isSessionWithAddTracks(session)) {
+                return;
+            }
+            setError(undefined);
+            model.setError(undefined);
+            transaction(() => {
+                if (sessionTrackData) {
+                    session.addTrackConf(sessionTrackData);
+                    model.toggleTrack(sessionTrackData.trackId);
+                }
+                else if (showTrackId) {
+                    model.showTrack(showTrackId);
+                }
+                model.setViews([
+                    { bpPerPx: 0.1, offsetPx: 0 },
+                    { bpPerPx: 0.1, offsetPx: 0 },
+                ]);
+                model.setAssemblyNames(assembly2, assembly1);
+            });
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }
+    // this is a combination of any displayed error message we have
+    const displayError = error || model.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(Typography, { style: { textAlign: 'center' } }, "Select assemblies for dotplot 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 })))));
+});
+export default DotplotImportForm;
+//# sourceMappingURL=ImportForm.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ImportForm.js","sourceRoot":"","sources":["../../../src/DotplotView/components/ImportForm.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAClD,OAAO,EACL,MAAM,EACN,SAAS,EACT,WAAW,EACX,SAAS,EACT,gBAAgB,EAChB,IAAI,EACJ,KAAK,EACL,KAAK,EACL,UAAU,EACV,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,WAAW,EAAE,MAAM,MAAM,CAAA;AAGlC,OAAO,EAAE,UAAU,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AACvE,OAAO,EAAE,YAAY,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAA;AAIjE,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,0BAA0B,MAAM,8BAA8B,CAAA;AAErE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,mBAAmB,EAAE;QACnB,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,MAAM,EAAE,QAAQ;KACjB;IACD,gBAAgB,EAAE;QAChB,KAAK,EAAE,KAAK;QACZ,MAAM,EAAE,QAAQ;KACjB;CACF,CAAC,CAAC,CAAA;AAIH,SAAS,aAAa,CAAC,EACrB,mBAAmB,EACnB,cAAc,EACd,gBAAgB,EAChB,SAAS,EACT,SAAS,EACT,KAAK,GAQN;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAA;IAE5C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,MAAM,KAAK,MAAM,EAAE;YACrB,mBAAmB,CAAC,SAAS,CAAC,CAAA;YAC9B,cAAc,CAAC,SAAS,CAAC,CAAA;SAC1B;IACH,CAAC,EAAE,CAAC,MAAM,EAAE,mBAAmB,EAAE,cAAc,CAAC,CAAC,CAAA;IACjD,OAAO,CACL;QACE,oBAAC,WAAW;YACV,oBAAC,SAAS,IAAC,EAAE,EAAC,aAAa,+CAEf;YACZ,oBAAC,UAAU,IACT,GAAG,QACH,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,qBAChC,aAAa;gBAE7B,oBAAC,gBAAgB,IAAC,KAAK,EAAC,MAAM,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,MAAM,GAAG;gBAClE,oBAAC,gBAAgB,IACf,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,gBAAgB,GACtB;gBACF,oBAAC,gBAAgB,IACf,KAAK,EAAC,QAAQ,EACd,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,WAAW,GACjB,CACS,CACD;QACb,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,CACrB,oBAAC,iBAAiB,IAChB,mBAAmB,EAAE,mBAAmB,EACxC,gBAAgB,EAAE,gBAAgB,EAClC,SAAS,EAAE,SAAS,EACpB,SAAS,EAAE,SAAS,GACpB,CACH,CAAC,CAAC,CAAC,IAAI;QACP,MAAM,KAAK,WAAW,CAAC,CAAC,CAAC,CACxB,oBAAC,0BAA0B,IACzB,KAAK,EAAE,KAAK,EACZ,SAAS,EAAE,SAAS,EACpB,SAAS,EAAE,SAAS,EACpB,cAAc,EAAE,cAAc,GAC9B,CACH,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC;AAED,MAAM,iBAAiB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA+B,EAAE,EAAE;IAC5E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,OAAO,CAAA;IACjC,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;IAClE,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;IAClE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,EAAQ,CAAA;IAChE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,EAAU,CAAA;IAExD,SAAS,WAAW;QAClB,IAAI;YACF,IAAI,CAAC,sBAAsB,CAAC,OAAO,CAAC,EAAE;gBACpC,OAAM;aACP;YACD,QAAQ,CAAC,SAAS,CAAC,CAAA;YACnB,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;YACzB,WAAW,CAAC,GAAG,EAAE;gBACf,IAAI,gBAAgB,EAAE;oBACpB,OAAO,CAAC,YAAY,CAAC,gBAAgB,CAAC,CAAA;oBACtC,KAAK,CAAC,WAAW,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAA;iBAC5C;qBAAM,IAAI,WAAW,EAAE;oBACtB,KAAK,CAAC,SAAS,CAAC,WAAW,CAAC,CAAA;iBAC7B;gBAED,KAAK,CAAC,QAAQ,CAAC;oBACb,EAAE,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE;oBAC7B,EAAE,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE;iBAC9B,CAAC,CAAA;gBACF,KAAK,CAAC,gBAAgB,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;YAC9C,CAAC,CAAC,CAAA;SACH;QAAC,OAAO,CAAC,EAAE;YACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;SACZ;IACH,CAAC;IAED,+DAA+D;IAC/D,MAAM,YAAY,GAAG,KAAK,IAAI,KAAK,CAAC,KAAK,CAAA;IACzC,OAAO,CACL,oBAAC,SAAS,IAAC,SAAS,EAAE,OAAO,CAAC,mBAAmB;QAC9C,YAAY,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,YAAY,GAAI,CAAC,CAAC,CAAC,IAAI;QAC5D,oBAAC,IAAI,IACH,SAAS,QACT,OAAO,EAAE,CAAC,EACV,cAAc,EAAC,QAAQ,EACvB,UAAU,EAAC,QAAQ,EACnB,SAAS,EAAE,OAAO,CAAC,gBAAgB;YAEnC,oBAAC,IAAI,IAAC,IAAI;gBACR,oBAAC,KAAK,IAAC,KAAK,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;oBAC3B,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,yCAE7B;oBACb,oBAAC,IAAI,IACH,SAAS,QACT,OAAO,EAAE,CAAC,EACV,cAAc,EAAC,QAAQ,EACvB,UAAU,EAAC,QAAQ;wBAEnB,oBAAC,IAAI,IAAC,IAAI;4BACR,oBAAC,gBAAgB,IACf,QAAQ,EAAE,SAAS,EACnB,QAAQ,EAAE,GAAG,CAAC,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAClC,OAAO,EAAE,OAAO,GAChB,CACG;wBACP,oBAAC,IAAI,IAAC,IAAI;4BACR,oBAAC,gBAAgB,IACf,QAAQ,EAAE,SAAS,EACnB,QAAQ,EAAE,GAAG,CAAC,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAClC,OAAO,EAAE,OAAO,GAChB,CACG;wBACP,oBAAC,IAAI,IAAC,IAAI;4BACR,oBAAC,WAAW;gCACV,oBAAC,MAAM,IACL,OAAO,EAAE,WAAW,EACpB,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,aAGR,CACG,CACT,CACF,CACD;gBACR,oBAAC,aAAa,IACZ,cAAc,EAAE,cAAc,EAC9B,SAAS,EAAE,SAAS,EACpB,SAAS,EAAE,SAAS,EACpB,mBAAmB,EAAE,mBAAmB,EACxC,gBAAgB,EAAE,gBAAgB,EAClC,KAAK,EAAE,KAAK,GACZ,CACG,CACF,CACG,CACb,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

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

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