react-msaview 1.3.2 → 2.1.0

package/dist/components/TreeCanvasBlock.js

@@ -0,0 +1,252 @@
+import React, { useEffect, useRef, useState } from 'react';
+import { observer } from 'mobx-react';
+import RBush from 'rbush';
+import TreeMenu from './TreeMenu';
+import TreeBranchMenu from './TreeBranchMenu';
+const extendBounds = 5;
+const radius = 3.5;
+const d = radius * 2;
+const padding = 600;
+const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
+    const ref = useRef(null);
+    const clickMap = useRef(new RBush());
+    const mouseoverRef = useRef(null);
+    const [branchMenu, setBranchMenu] = useState();
+    const [toggleNodeMenu, setToggleNodeMenu] = useState();
+    const [hoverElt, setHoverElt] = useState();
+    const { hierarchy, rowHeight, scrollY, treeWidth, showBranchLen, collapsed, margin, labelsAlignRight, noTree, blockSize, drawNodeBubbles, drawTree, treeAreaWidth, structures, highResScaleFactor, } = model;
+    useEffect(() => {
+        clickMap.current.clear();
+        if (!ref.current) {
+            return;
+        }
+        const ctx = ref.current.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        ctx.resetTransform();
+        ctx.scale(highResScaleFactor, highResScaleFactor);
+        ctx.clearRect(0, 0, treeWidth + padding, blockSize);
+        ctx.translate(margin.left, -offsetY);
+        const font = ctx.font;
+        ctx.font = font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
+        if (!noTree && drawTree) {
+            for (const { source, target } of hierarchy.links()) {
+                const y = showBranchLen ? 'len' : 'y';
+                // @ts-expect-error
+                const { x: sy, [y]: sx } = source;
+                // @ts-expect-error
+                const { x: ty, [y]: tx } = target;
+                const y1 = Math.min(sy, ty);
+                const y2 = Math.max(sy, ty);
+                // 1d line intersection to check if line crosses block at all, this is
+                // an optimization that allows us to skip drawing most tree links
+                // outside the block
+                if (offsetY + blockSize >= y1 && y2 >= offsetY) {
+                    ctx.beginPath();
+                    ctx.moveTo(sx, sy);
+                    ctx.lineTo(sx, ty);
+                    ctx.lineTo(tx, ty);
+                    ctx.stroke();
+                }
+            }
+            if (drawNodeBubbles) {
+                for (const node of hierarchy.descendants()) {
+                    const val = showBranchLen ? 'len' : 'y';
+                    const { 
+                    // @ts-expect-error
+                    x: y, 
+                    // @ts-expect-error
+                    [val]: x, data, } = node;
+                    const { id = '', name = '' } = data;
+                    if (y > offsetY - extendBounds &&
+                        y < offsetY + blockSize + extendBounds) {
+                        ctx.strokeStyle = 'black';
+                        ctx.fillStyle = collapsed.includes(id) ? 'black' : 'white';
+                        ctx.beginPath();
+                        ctx.arc(x, y, radius, 0, 2 * Math.PI);
+                        ctx.fill();
+                        ctx.stroke();
+                        clickMap.current.insert({
+                            minX: x - radius,
+                            maxX: x - radius + d,
+                            minY: y - radius,
+                            maxY: y - radius + d,
+                            branch: true,
+                            id,
+                            name,
+                        });
+                    }
+                }
+            }
+        }
+        if (rowHeight >= 5) {
+            if (labelsAlignRight) {
+                ctx.textAlign = 'right';
+                ctx.setLineDash([1, 3]);
+            }
+            else {
+                ctx.textAlign = 'start';
+            }
+            for (const node of hierarchy.leaves()) {
+                const { 
+                // @ts-expect-error
+                x: y, 
+                // @ts-expect-error
+                y: x, data: { name, id }, 
+                // @ts-expect-error
+                len, } = node;
+                if (y > offsetY - extendBounds &&
+                    y < offsetY + blockSize + extendBounds) {
+                    // note: +rowHeight/4 matches with -rowHeight/4 in msa
+                    const yp = y + rowHeight / 4;
+                    const xp = showBranchLen ? len : x;
+                    const { width } = ctx.measureText(name);
+                    const height = ctx.measureText('M').width; // use an 'em' for height
+                    const hasStructure = structures[name];
+                    ctx.fillStyle = hasStructure ? 'blue' : 'black';
+                    if (!drawTree && !labelsAlignRight) {
+                        ctx.fillText(name, 0, yp);
+                        clickMap.current.insert({
+                            minX: 0,
+                            maxX: width,
+                            minY: yp - height,
+                            maxY: yp,
+                            name,
+                            id,
+                        });
+                    }
+                    else if (labelsAlignRight) {
+                        const smallPadding = 2;
+                        const offset = treeAreaWidth - smallPadding - margin.left;
+                        if (drawTree && !noTree) {
+                            const { width } = ctx.measureText(name);
+                            ctx.moveTo(xp + radius + 2, y);
+                            ctx.lineTo(offset - smallPadding - width, y);
+                            ctx.stroke();
+                        }
+                        ctx.fillText(name, offset, yp);
+                        clickMap.current.insert({
+                            minX: treeAreaWidth - margin.left - width,
+                            maxX: treeAreaWidth - margin.left,
+                            minY: yp - height,
+                            maxY: yp,
+                            name,
+                            id,
+                        });
+                    }
+                    else {
+                        ctx.fillText(name, xp + d, yp);
+                        clickMap.current.insert({
+                            minX: xp + d,
+                            maxX: xp + d + width,
+                            minY: yp - height,
+                            maxY: yp,
+                            name,
+                            id,
+                        });
+                    }
+                }
+            }
+            ctx.setLineDash([]);
+        }
+    }, [
+        collapsed,
+        rowHeight,
+        margin.left,
+        hierarchy,
+        offsetY,
+        treeWidth,
+        showBranchLen,
+        noTree,
+        blockSize,
+        drawNodeBubbles,
+        drawTree,
+        labelsAlignRight,
+        treeAreaWidth,
+        structures,
+        highResScaleFactor,
+    ]);
+    useEffect(() => {
+        const canvas = mouseoverRef.current;
+        if (!canvas) {
+            return;
+        }
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        ctx.resetTransform();
+        ctx.clearRect(0, 0, treeWidth + padding, blockSize);
+        ctx.translate(margin.left, -offsetY);
+        if (hoverElt) {
+            const { minX, maxX, minY, maxY } = hoverElt;
+            ctx.fillStyle = 'rgba(0,0,0,0.1)';
+            ctx.fillRect(minX, minY, maxX - minX, maxY - minY);
+        }
+    }, [hoverElt, margin.left, offsetY, blockSize, treeWidth]);
+    function hoverBranchClickMap(event) {
+        const x = event.nativeEvent.offsetX - margin.left;
+        const y = event.nativeEvent.offsetY;
+        const [entry] = clickMap.current.search({
+            minX: x,
+            maxX: x + 1,
+            minY: y + offsetY,
+            maxY: y + 1 + offsetY,
+        });
+        return entry && entry.branch
+            ? { ...entry, x: event.clientX, y: event.clientY }
+            : undefined;
+    }
+    function hoverNameClickMap(event) {
+        const x = event.nativeEvent.offsetX - margin.left;
+        const y = event.nativeEvent.offsetY;
+        const [entry] = clickMap.current.search({
+            minX: x,
+            maxX: x + 1,
+            minY: y + offsetY,
+            maxY: y + 1 + offsetY,
+        });
+        return entry && !entry.branch
+            ? { ...entry, x: event.clientX, y: event.clientY }
+            : undefined;
+    }
+    return (React.createElement(React.Fragment, null,
+        (branchMenu === null || branchMenu === void 0 ? void 0 : branchMenu.id) ? (React.createElement(TreeBranchMenu, { node: branchMenu, model: model, onClose: () => setBranchMenu(undefined) })) : null,
+        (toggleNodeMenu === null || toggleNodeMenu === void 0 ? void 0 : toggleNodeMenu.id) ? (React.createElement(TreeMenu, { node: toggleNodeMenu, model: model, onClose: () => setToggleNodeMenu(undefined) })) : null,
+        React.createElement("canvas", { width: (treeWidth + padding) * highResScaleFactor, height: blockSize * highResScaleFactor, style: {
+                width: treeWidth + padding,
+                height: blockSize,
+                top: scrollY + offsetY,
+                left: 0,
+                position: 'absolute',
+            }, onMouseMove: event => {
+                if (!ref.current) {
+                    return;
+                }
+                const ret = hoverNameClickMap(event) || hoverBranchClickMap(event);
+                ref.current.style.cursor = ret ? 'pointer' : 'default';
+                setHoverElt(hoverNameClickMap(event));
+            }, onClick: event => {
+                const { clientX: x, clientY: y } = event;
+                const data = hoverBranchClickMap(event);
+                if (data === null || data === void 0 ? void 0 : data.id) {
+                    setBranchMenu({ ...data, x, y });
+                }
+                const data2 = hoverNameClickMap(event);
+                if (data2 === null || data2 === void 0 ? void 0 : data2.id) {
+                    setToggleNodeMenu({ ...data2, x, y });
+                }
+            }, ref: ref }),
+        React.createElement("canvas", { style: {
+                width: treeWidth + padding,
+                height: blockSize,
+                top: scrollY + offsetY,
+                left: 0,
+                position: 'absolute',
+                pointerEvents: 'none',
+                zIndex: 100,
+            }, width: treeWidth + padding, height: blockSize, ref: mouseoverRef })));
+});
+export default TreeCanvasBlock;
+//# sourceMappingURL=TreeCanvasBlock.js.map

package/dist/components/TreeCanvasBlock.js.map

@@ -0,0 +1 @@
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package/dist/components/TreeMenu.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+import { MsaViewModel } from '../model';
+declare const TreeMenu: ({ node, onClose, model, }: {
+    node: {
+        x: number;
+        y: number;
+        name: string;
+    };
+    model: MsaViewModel;
+    onClose: () => void;
+}) => React.JSX.Element;
+export default TreeMenu;

package/dist/components/TreeMenu.js

@@ -0,0 +1,56 @@
+import React, { lazy } from 'react';
+import { Menu, MenuItem } from '@mui/material';
+import { observer } from 'mobx-react';
+const MoreInfoDlg = lazy(() => import('./dialogs/MoreInfoDlg'));
+const TreeMenu = observer(function ({ node, onClose, model, }) {
+    var _a, _b;
+    const { structures } = model;
+    const nodeDetails = node ? model.getRowData(node.name) : undefined;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+                top: node.y,
+                left: node.x,
+            }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
+            React.createElement(MenuItem, { dense: true, disabled: true }, node.name),
+            React.createElement(MenuItem, { dense: true, onClick: () => {
+                    model.setDialogComponent(MoreInfoDlg, {
+                        info: model.getRowData(node.name),
+                    });
+                    onClose();
+                } }, "More info..."), (_a = structures[node.name]) === null || _a === void 0 ? void 0 :
+            _a.map(entry => {
+                return !model.selectedStructures.some(n => n.id === node.name) ? (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
+                        model.addStructureToSelection({
+                            structure: entry,
+                            id: node.name,
+                        });
+                        onClose();
+                    } },
+                    "Add PDB to selection (",
+                    entry.pdb,
+                    ")")) : (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
+                        model.removeStructureFromSelection({
+                            structure: entry,
+                            id: node.name,
+                        });
+                        onClose();
+                    } },
+                    "Remove PDB from selection (",
+                    entry.pdb,
+                    ")"));
+            }), // @ts-expect-error
+        (_b = nodeDetails === null || nodeDetails === void 0 ? void 0 : nodeDetails.data.accession) === null || _b === void 0 ? void 0 :
+            _b.map(accession => (React.createElement(MenuItem, { dense: true, key: accession, onClick: () => {
+                    model.addUniprotTrack({
+                        // @ts-expect-error
+                        name: nodeDetails === null || nodeDetails === void 0 ? void 0 : nodeDetails.data.name,
+                        accession,
+                    });
+                    onClose();
+                } },
+                "Open UniProt track (",
+                accession,
+                ")"))))));
+});
+export default TreeMenu;
+//# sourceMappingURL=TreeMenu.js.map

package/dist/components/TreeMenu.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"TreeMenu.js","sourceRoot":"","sources":["../../src/components/TreeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,uBAAuB,CAAC,CAAC,CAAA;AAE/D,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,OAAO,EACP,KAAK,GAKN;;IACC,MAAM,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAC5B,MAAM,WAAW,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAElE,OAAO,CACL;QACE,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;gBACd,GAAG,EAAE,IAAI,CAAC,CAAC;gBACX,IAAI,EAAE,IAAI,CAAC,CAAC;aACb,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;YAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CAAC,IAAI,CACD;YAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,kBAAkB,CAAC,WAAW,EAAE;wBACpC,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC;qBAClC,CAAC,CAAA;oBACF,OAAO,EAAE,CAAA;gBACX,CAAC,mBAGQ,EAEV,MAAA,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC;eAAE,GAAG,CAAC,KAAK,CAAC,EAAE;gBAClC,OAAO,CAAC,KAAK,CAAC,kBAAkB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAC/D,oBAAC,QAAQ,IACP,GAAG,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAC1B,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,uBAAuB,CAAC;4BAC5B,SAAS,EAAE,KAAK;4BAChB,EAAE,EAAE,IAAI,CAAC,IAAI;yBACd,CAAC,CAAA;wBACF,OAAO,EAAE,CAAA;oBACX,CAAC;;oBAEsB,KAAK,CAAC,GAAG;wBACvB,CACZ,CAAC,CAAC,CAAC,CACF,oBAAC,QAAQ,IACP,GAAG,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAC1B,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,4BAA4B,CAAC;4BACjC,SAAS,EAAE,KAAK;4BAChB,EAAE,EAAE,IAAI,CAAC,IAAI;yBACd,CAAC,CAAA;wBACF,OAAO,EAAE,CAAA;oBACX,CAAC;;oBAE2B,KAAK,CAAC,GAAG;wBAC5B,CACZ,CAAA;YACH,CAAC,CAAC,EAED,mBAAmB;QACpB,MAAA,WAAW,aAAX,WAAW,uBAAX,WAAW,CAAE,IAAI,CAAC,SAAS;eAAE,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC5C,oBAAC,QAAQ,IACP,KAAK,QACL,GAAG,EAAE,SAAS,EACd,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,eAAe,CAAC;wBACpB,mBAAmB;wBACnB,IAAI,EAAE,WAAW,aAAX,WAAW,uBAAX,WAAW,CAAE,IAAI,CAAC,IAAI;wBAC5B,SAAS;qBACV,CAAC,CAAA;oBACF,OAAO,EAAE,CAAA;gBACX,CAAC;;gBAEoB,SAAS;oBACrB,CACZ,CAAC,CACG,CACN,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/TreeRuler.d.ts

@@ -1,6 +1,6 @@
-/// <reference types="react" />
+import React from 'react';
 import { MsaViewModel } from '../model';
 declare const TreeRuler: ({ model }: {
     model: MsaViewModel;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default TreeRuler;

package/dist/components/TreeRuler.js

@@ -1,8 +1,8 @@
 import React from 'react';
 import { observer } from 'mobx-react';
-var TreeRuler = observer(function (_a) {
-    var model = _a.model;
-    var treeWidth = model.treeWidth;
+const TreeRuler = observer(({ model }) => {
+    const { treeWidth } = model;
     return React.createElement("div", { style: { width: treeWidth } });
 });
 export default TreeRuler;
+//# sourceMappingURL=TreeRuler.js.map

package/dist/components/TreeRuler.js.map

@@ -0,0 +1 @@
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package/dist/components/VerticalGuide.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { MsaViewModel } from '../model';
+declare const VerticalGuide: ({ model, coordX, }: {
+    model: MsaViewModel;
+    coordX: number;
+}) => React.JSX.Element;
+export default VerticalGuide;

package/dist/components/VerticalGuide.js

@@ -0,0 +1,30 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { Tooltip } from '@mui/material';
+const useStyles = makeStyles()({
+    guide: {
+        pointerEvents: 'none',
+        height: '100%',
+        width: 1,
+        position: 'absolute',
+        zIndex: 10,
+    },
+});
+const VerticalGuide = observer(function ({ model, coordX, }) {
+    const { treeAreaWidth } = model;
+    const { classes } = useStyles();
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Tooltip, { open: true, placement: "top", title: `${model.pxToBp(coordX) + 1}`, arrow: true },
+            React.createElement("div", { style: {
+                    left: coordX + treeAreaWidth,
+                    position: 'absolute',
+                    height: 1,
+                } })),
+        React.createElement("div", { className: classes.guide, style: {
+                left: coordX + treeAreaWidth,
+                background: 'red',
+            } })));
+});
+export default VerticalGuide;
+//# sourceMappingURL=VerticalGuide.js.map

package/dist/components/VerticalGuide.js.map

@@ -0,0 +1 @@
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package/dist/components/ZoomControls.d.ts

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

package/dist/components/ZoomControls.js

@@ -0,0 +1,58 @@
+import React from 'react';
+import { IconButton } from '@mui/material';
+import { observer } from 'mobx-react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+// icons
+import MoreVert from '@mui/icons-material/MoreVert';
+import ZoomIn from '@mui/icons-material/ZoomIn';
+import ZoomOut from '@mui/icons-material/ZoomOut';
+const ZoomControls = observer(function ZoomControls({ model, }) {
+    const { colWidth, rowHeight } = model;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(IconButton, { onClick: () => {
+                model.setColWidth(Math.ceil(colWidth * 1.5));
+                model.setRowHeight(Math.ceil(rowHeight * 1.5));
+            } },
+            React.createElement(ZoomIn, null)),
+        React.createElement(IconButton, { onClick: () => {
+                model.setColWidth(Math.max(1, Math.floor(colWidth * 0.75)));
+                model.setRowHeight(Math.max(1.5, Math.floor(rowHeight * 0.75)));
+            } },
+            React.createElement(ZoomOut, null)),
+        React.createElement(CascadingMenuButton, { menuItems: [
+                {
+                    label: 'Decrease row height',
+                    onClick: () => {
+                        model.setRowHeight(Math.max(1.5, rowHeight * 0.75));
+                    },
+                },
+                {
+                    label: 'Increase row height',
+                    onClick: () => {
+                        model.setRowHeight(rowHeight * 1.5);
+                    },
+                },
+                {
+                    label: 'Decrease col width',
+                    onClick: () => {
+                        model.setColWidth(Math.max(1, colWidth * 0.75));
+                    },
+                },
+                {
+                    label: 'Increase col width',
+                    onClick: () => {
+                        model.setColWidth(colWidth * 1.5);
+                    },
+                },
+                {
+                    label: 'Reset zoom to default',
+                    onClick: () => {
+                        model.setColWidth(16);
+                        model.setRowHeight(20);
+                    },
+                },
+            ] },
+            React.createElement(MoreVert, null))));
+});
+export default ZoomControls;
+//# sourceMappingURL=ZoomControls.js.map

package/dist/components/ZoomControls.js.map

@@ -0,0 +1 @@
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package/dist/components/data/seq2.d.ts

@@ -1,3 +1,3 @@
-export const smallMSA: "CLUSTAL O(1.2.3) multiple sequence alignment\nUniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM\nUniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI\nUniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM\nUniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM\nUniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM\nUniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------\nUniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS\nUniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV\nUniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP\nUniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------\nUniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST\nUniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------\n";
-export const smallMSAOnly: "CLUSTAL O(1.2.4) multiple sequence alignment\n\n\nsp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\t60\nsp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG\t60\nsp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG\t60\n                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**\n\nsp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\t120\nsp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP\t120\nsp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA\t120\n                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**\n\nsp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR\t142\n                           .**: ****: ** ***.***";
-export const smallTree: "(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)";
+export declare const smallMSA = "CLUSTAL O(1.2.3) multiple sequence alignment\nUniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM\nUniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI\nUniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM\nUniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM\nUniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM\nUniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------\nUniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS\nUniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV\nUniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP\nUniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------\nUniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST\nUniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------\n";
+export declare const smallMSAOnly = "CLUSTAL O(1.2.4) multiple sequence alignment\n\n\nsp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\t60\nsp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG\t60\nsp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG\t60\n                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**\n\nsp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\t120\nsp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP\t120\nsp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA\t120\n                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**\n\nsp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR\t142\n                           .**: ****: ** ***.***";
+export declare const smallTree = "(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)";

package/dist/components/data/seq2.js

@@ -1,3 +1,33 @@
-export var smallMSA = "CLUSTAL O(1.2.3) multiple sequence alignment\nUniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM\nUniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI\nUniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM\nUniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM\nUniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM\nUniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------\nUniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS\nUniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV\nUniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP\nUniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------\nUniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST\nUniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------\n";
-export var smallMSAOnly = "CLUSTAL O(1.2.4) multiple sequence alignment\n\n\nsp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\t60\nsp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG\t60\nsp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG\t60\n                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**\n\nsp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\t120\nsp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP\t120\nsp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA\t120\n                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**\n\nsp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR\t142\n                           .**: ****: ** ***.***";
-export var smallTree = '(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)';
+export const smallMSA = `CLUSTAL O(1.2.3) multiple sequence alignment
+UniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
+UniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
+UniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
+UniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM
+UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM
+UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------
+UniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS
+UniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV
+UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP
+UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
+UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
+UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
+`;
+export const smallMSAOnly = `CLUSTAL O(1.2.4) multiple sequence alignment
+
+
+sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
+sp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG	60
+sp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG	60
+                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**
+
+sp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP	120
+sp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP	120
+sp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA	120
+                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**
+
+sp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR	142
+sp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR	142
+sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
+                           .**: ****: ** ***.***`;
+export const smallTree = '(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)';
+//# sourceMappingURL=seq2.js.map

package/dist/components/data/seq2.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seq2.js","sourceRoot":"","sources":["../../../src/components/data/seq2.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;;;;;;;;;;;;;CAavB,CAAA;AAED,MAAM,CAAC,MAAM,YAAY,GAAG;;;;;;;;;;;;;;;;iDAgBqB,CAAA;AAEjD,MAAM,CAAC,MAAM,SAAS,GACpB,+nBAA+nB,CAAA"}

package/dist/components/dialogs/AboutDlg.d.ts

@@ -0,0 +1,4 @@
+import React from 'react';
+export default function AboutDialog({ onClose }: {
+    onClose: () => void;
+}): React.JSX.Element;

package/dist/components/dialogs/AboutDlg.js

@@ -0,0 +1,40 @@
+import React from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { DialogContent, Typography, Link } from '@mui/material';
+import { version } from '../../version';
+export default function AboutDialog({ onClose }) {
+    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "About this plugin" },
+        React.createElement(DialogContent, null,
+            React.createElement(Typography, null,
+                "MSAView ",
+                version,
+                " (",
+                React.createElement(Link, { href: "https://github.com/gmod/jbrowse-plugin-msaview" }, "Github"),
+                ")"),
+            React.createElement("ul", null,
+                React.createElement("li", null,
+                    React.createElement(Typography, null,
+                        "We use some color schemes from the",
+                        ' ',
+                        React.createElement(Link, { href: "https://github.com/biotite-dev/biotite" }, "biotite"),
+                        ' ',
+                        "project, and their license is reproduced",
+                        ' ',
+                        React.createElement(Link, { href: "https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst" }, "here"))),
+                React.createElement("li", null,
+                    React.createElement(Typography, null,
+                        "See this page for some information on jalview colorings",
+                        ' ',
+                        React.createElement(Link, { href: "https://www.jalview.org/help/html/colourSchemes/" }, "here"))),
+                React.createElement("li", null,
+                    React.createElement(Typography, null,
+                        "See this page for some info on the clustal, cinema, maeditor, and lesk color schemes",
+                        ' ',
+                        React.createElement(Link, { href: "http://www.bioinformatics.nl/~berndb/aacolour.html" }, "here"))),
+                React.createElement("li", null,
+                    React.createElement(Typography, null,
+                        "See this paper about the flower color scheme",
+                        ' ',
+                        React.createElement(Link, { href: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/" }, "here")))))));
+}
+//# sourceMappingURL=AboutDlg.js.map

package/dist/components/dialogs/AboutDlg.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"AboutDlg.js","sourceRoot":"","sources":["../../../src/components/dialogs/AboutDlg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,aAAa,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAC/D,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAEvC,MAAM,CAAC,OAAO,UAAU,WAAW,CAAC,EAAE,OAAO,EAA2B;IACtE,OAAO,CACL,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,QAAC,KAAK,EAAC,mBAAmB;QAC9D,oBAAC,aAAa;YACZ,oBAAC,UAAU;;gBACA,OAAO;;gBAChB,oBAAC,IAAI,IAAC,IAAI,EAAC,gDAAgD,aAEpD;oBAEI;YAEb;gBACE;oBACE,oBAAC,UAAU;;wBAC0B,GAAG;wBACtC,oBAAC,IAAI,IAAC,IAAI,EAAC,wCAAwC,cAAe;wBAAC,GAAG;;wBAC7B,GAAG;wBAC5C,oBAAC,IAAI,IAAC,IAAI,EAAC,gEAAgE,WAEpE,CACI,CACV;gBACL;oBACE,oBAAC,UAAU;;wBAC+C,GAAG;wBAC3D,oBAAC,IAAI,IAAC,IAAI,EAAC,kDAAkD,WAEtD,CACI,CACV;gBACL;oBACE,oBAAC,UAAU;;wBAEU,GAAG;wBACtB,oBAAC,IAAI,IAAC,IAAI,EAAC,oDAAoD,WAExD,CACI,CACV;gBACL;oBACE,oBAAC,UAAU;;wBACoC,GAAG;wBAChD,oBAAC,IAAI,IAAC,IAAI,EAAC,uDAAuD,WAE3D,CACI,CACV,CACF,CACS,CACT,CACV,CAAA;AACH,CAAC"}

package/{bundle/components → dist/components/dialogs}/AddTrackDlg.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
-import { MsaViewModel } from '../model';
+import React from 'react';
+import { MsaViewModel } from '../../model';
 declare const _default: ({ model, onClose, open, }: {
     model: MsaViewModel;
     onClose: () => void;
     open: boolean;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;