react-msaview 8.4.1 → 9.1.0

package/dist/components/dialogs/ExportSVGDialog.js

@@ -2,6 +2,7 @@ import React, { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
 import { Alert, Button, CircularProgress, DialogActions, DialogContent, FormControl, FormControlLabel, FormLabel, Radio, RadioGroup, Typography, useTheme, } from '@mui/material';
 import { observer } from 'mobx-react';
+import { exportPageSize, getLayout } from '../../exportLayout.js';
 import Checkbox2 from '../Checkbox2.js';
 // Run after the browser has painted. A requestAnimationFrame callback still
 // runs *before* the frame it was queued for, so one alone hands the main thread
@@ -19,12 +20,9 @@ const ExportSVGDialog = observer(function ({ model, onClose, }) {
     const [error, setError] = useState();
     const [exporting, setExporting] = useState(false);
     const theme = useTheme();
-    const { totalWidth, totalHeight, treeAreaWidth, rowPanelsWidth, turnedOnTracks, totalTrackAreaHeight, numColumns, leaves, showMsaLetters, treeOverviewHeight, } = model;
+    const { turnedOnTracks, numColumns, leaves, showMsaLetters } = model;
     const hasTracks = turnedOnTracks.length > 0;
-    const entireWidth = totalWidth + treeAreaWidth + rowPanelsWidth;
-    const entireHeight = totalHeight +
-        (includeTracks ? totalTrackAreaHeight : 0) +
-        treeOverviewHeight;
+    const entire = exportPageSize(model, getLayout(model, { theme, exportType: 'entire', includeTracks }));
     // the background is one raster image whatever its size, so what the figure
     // actually costs is its residue letters: each is an svg element of its own.
     // Past roughly this many the export runs to tens of seconds and can exhaust
@@ -56,9 +54,9 @@ const ExportSVGDialog = observer(function ({ model, onClose, }) {
                         React.createElement(FormControlLabel, { value: "viewport", control: React.createElement(Radio, null), label: "Current viewport only" })))),
             isLargeExport ? (React.createElement(Alert, { severity: "warning", style: { marginTop: 8 } },
                 "The entire MSA is ",
-                Math.round(entireWidth),
+                Math.round(entire.width),
                 "x",
-                Math.round(entireHeight),
+                Math.round(entire.height),
                 " pixels and draws",
                 ' ',
                 Math.round(glyphs / 1000),

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

@@ -1 +1 @@
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package/dist/components/dialogs/HelpDialog.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+export default function HelpDialog({ model, onClose, }: {
+    model: MsaViewModel;
+    onClose: () => void;
+}): React.JSX.Element;

package/dist/components/dialogs/HelpDialog.js

@@ -0,0 +1,30 @@
+import React, { lazy } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, Table, TableBody, TableCell, TableRow, Typography, } from '@mui/material';
+import { version } from '../../version.js';
+import { keyboardControls, mouseControls } from '../controls.js';
+const AboutDialog = lazy(() => import('./AboutDialog.js'));
+function ControlTable({ title, rows }) {
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Typography, { variant: "subtitle2", sx: { mt: 1 } }, title),
+        React.createElement(Table, { size: "small", "aria-label": title },
+            React.createElement(TableBody, null, rows.map(({ label, action }) => (React.createElement(TableRow, { key: label },
+                React.createElement(TableCell, { sx: { whiteSpace: 'nowrap', fontWeight: 500 } }, label),
+                React.createElement(TableCell, null, action))))))));
+}
+export default function HelpDialog({ model, onClose, }) {
+    return (React.createElement(Dialog, { open: true, title: "Mouse & keyboard", onClose: onClose },
+        React.createElement(DialogContent, null,
+            React.createElement(ControlTable, { title: "Mouse", rows: mouseControls }),
+            React.createElement(ControlTable, { title: "Keyboard (click the alignment first)", rows: keyboardControls })),
+        React.createElement(DialogActions, null,
+            React.createElement(Typography, { variant: "caption", sx: { mr: 'auto', pl: 1 } },
+                "MSAView ",
+                version),
+            React.createElement(Button, { onClick: () => {
+                    model.queueDialog(done => [AboutDialog, { onClose: done }]);
+                    onClose();
+                } }, "About & credits"),
+            React.createElement(Button, { variant: "contained", onClick: onClose }, "Close"))));
+}
+//# sourceMappingURL=HelpDialog.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/HelpDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,KAAK,EACL,SAAS,EACT,SAAS,EACT,QAAQ,EACR,UAAU,GACX,MAAM,eAAe,CAAA;AAEtB,OAAO,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,gBAAgB,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAA;AAKhE,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,kBAAmB,CAAC,CAAC,CAAA;AAE3D,SAAS,YAAY,CAAC,EAAE,KAAK,EAAE,IAAI,EAAsC;IACvE,OAAO,CACL;QACE,oBAAC,UAAU,IAAC,OAAO,EAAC,WAAW,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,IAC1C,KAAK,CACK;QACb,oBAAC,KAAK,IAAC,IAAI,EAAC,OAAO,gBAAa,KAAK;YACnC,oBAAC,SAAS,QACP,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAC/B,oBAAC,QAAQ,IAAC,GAAG,EAAE,KAAK;gBAClB,oBAAC,SAAS,IAAC,EAAE,EAAE,EAAE,UAAU,EAAE,QAAQ,EAAE,UAAU,EAAE,GAAG,EAAE,IACrD,KAAK,CACI;gBACZ,oBAAC,SAAS,QAAE,MAAM,CAAa,CACtB,CACZ,CAAC,CACQ,CACN,CACP,CACJ,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,KAAK,EACL,OAAO,GAIR;IACC,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,KAAK,EAAC,kBAAkB,EAAC,OAAO,EAAE,OAAO;QACpD,oBAAC,aAAa;YACZ,oBAAC,YAAY,IAAC,KAAK,EAAC,OAAO,EAAC,IAAI,EAAE,aAAa,GAAI;YACnD,oBAAC,YAAY,IACX,KAAK,EAAC,sCAAsC,EAC5C,IAAI,EAAE,gBAAgB,GACtB,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,UAAU,IAAC,OAAO,EAAC,SAAS,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,EAAE;;gBAC5C,OAAO,CACL;YACb,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,EAAE,CAAA;gBACX,CAAC,sBAGM;YACT,oBAAC,MAAM,IAAC,OAAO,EAAC,WAAW,EAAC,OAAO,EAAE,OAAO,YAEnC,CACK,CACT,CACV,CAAA;AACH,CAAC"}

package/dist/components/header/FileMenu.js

@@ -6,18 +6,43 @@ import FolderOpen from '@mui/icons-material/FolderOpen';
 import Menu from '@mui/icons-material/Menu';
 import PhotoCamera from '@mui/icons-material/PhotoCamera';
 import { observer } from 'mobx-react';
+import { maxNeighborJoiningRows } from '../../constants.js';
 import { getAnnotationsMenu } from './getAnnotationsMenu.js';
 const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog.js'));
 const ExportSVGDialog = lazy(() => import('../dialogs/ExportSVGDialog.js'));
+function neighborJoiningItem(model) {
+    const rows = model.rowMap.size;
+    const tooManyRows = rows > maxNeighborJoiningRows;
+    return {
+        label: tooManyRows
+            ? `Calculate neighbor joining tree (over ${maxNeighborJoiningRows} rows, use FastTree)`
+            : 'Calculate neighbor joining tree (BLOSUM62)',
+        icon: AccountTree,
+        disabled: tooManyRows || rows < 2,
+        onClick: () => {
+            try {
+                model.calculateNeighborJoiningTreeFromMSA();
+            }
+            catch (e) {
+                console.error('Failed to calculate NJ tree:', e);
+                model.addWarning(e instanceof Error ? e.message : String(e));
+            }
+        },
+    };
+}
 const FileMenu = observer(({ model }) => {
     return (React.createElement(CascadingMenuButton, { "data-testid": "file_menu", tooltip: "File", menuItems: [
-            {
-                label: 'Return to import form',
-                icon: FolderOpen,
-                onClick: () => {
-                    model.reset();
-                },
-            },
+            ...(model.importForm
+                ? [
+                    {
+                        label: 'Return to import form',
+                        icon: FolderOpen,
+                        onClick: () => {
+                            model.reset();
+                        },
+                    },
+                ]
+                : []),
             {
                 label: 'Metadata',
                 icon: Assignment,
@@ -38,6 +63,7 @@ const FileMenu = observer(({ model }) => {
                     model,
                 }),
             },
+            neighborJoiningItem(model),
             {
                 label: 'Export tree (Newick)',
                 icon: AccountTree,

package/dist/components/header/FileMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"FileMenu.js","sourceRoot":"","sources":["../../../src/components/header/FileMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AAC3D,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAA;AAI5D,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAC1E,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,+BAAgC,CAAC,CAAC,CAAA;AAE5E,SAAS,mBAAmB,CAAC,KAAmB;IAC9C,MAAM,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,IAAI,CAAA;IAC9B,MAAM,WAAW,GAAG,IAAI,GAAG,sBAAsB,CAAA;IACjD,OAAO;QACL,KAAK,EAAE,WAAW;YAChB,CAAC,CAAC,yCAAyC,sBAAsB,sBAAsB;YACvF,CAAC,CAAC,4CAA4C;QAChD,IAAI,EAAE,WAAW;QACjB,QAAQ,EAAE,WAAW,IAAI,IAAI,GAAG,CAAC;QACjC,OAAO,EAAE,GAAG,EAAE;YACZ,IAAI,CAAC;gBACH,KAAK,CAAC,mCAAmC,EAAE,CAAA;YAC7C,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;gBAChD,KAAK,CAAC,UAAU,CAAC,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;YAC9D,CAAC;QACH,CAAC;KACF,CAAA;AACH,CAAC;AAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAC/D,OAAO,CACL,oBAAC,mBAAmB,mBACN,WAAW,EACvB,OAAO,EAAC,MAAM,EACd,SAAS,EAAE;YACT,GAAG,CAAC,KAAK,CAAC,UAAU;gBAClB,CAAC,CAAC;oBACE;wBACE,KAAK,EAAE,uBAAuB;wBAC9B,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,KAAK,EAAE,CAAA;wBACf,CAAC;qBACF;iBACF;gBACH,CAAC,CAAC,EAAE,CAAC;YACP;gBACE,KAAK,EAAE,UAAU;gBACjB,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,cAAc;wBACd;4BACE,KAAK;4BACL,OAAO;yBACR;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;YACD;gBACE,KAAK,EAAE,aAAa;gBACpB,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE,kBAAkB,CAAC;oBAC1B,KAAK;iBACN,CAAC;aACH;YACD,mBAAmB,CAAC,KAAK,CAAC;YAC1B;gBACE,KAAK,EAAE,sBAAsB;gBAC7B,IAAI,EAAE,WAAW;gBACjB,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM;gBAC7B,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,YAAY,EAAE,CAAA;gBACtB,CAAC;aACF;YACD;gBACE,KAAK,EAAE,YAAY;gBACnB,IAAI,EAAE,WAAW;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf;4BACE,OAAO;4BACP,KAAK;yBACN;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;SACF,EACD,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE;QAExD,oBAAC,IAAI,OAAG,CACY,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/header/Header.js

@@ -16,8 +16,7 @@ import SelectionMenu from './SelectionMenu.js';
 import TreeSettingsMenu from './TreeSettingsMenu.js';
 import UnshareableDataWarning from './UnshareableDataWarning.js';
 import ZoomControls from './ZoomControls.js';
-import ZoomMenu from './ZoomMenu.js';
-const AboutDialog = lazy(() => import('../dialogs/AboutDialog.js'));
+const HelpDialog = lazy(() => import('../dialogs/HelpDialog.js'));
 const Header = observer(function ({ model }) {
     const [ref, { height }] = useMeasure();
     useEffect(() => {
@@ -32,7 +31,6 @@ const Header = observer(function ({ model }) {
         React.createElement(TreeSettingsMenu, { model: model }),
         React.createElement(MSASettingsMenu, { model: model }),
         React.createElement(ZoomControls, { model: model }),
-        React.createElement(ZoomMenu, { model: model }),
         React.createElement(GappynessSlider, { model: model }),
         React.createElement(GoToBox, { model: model }),
         React.createElement("div", { style: { paddingLeft: 20, margin: 'auto' } },
@@ -43,9 +41,9 @@ const Header = observer(function ({ model }) {
         React.createElement(LoadWarnings, { model: model }),
         React.createElement(UnshareableDataWarning, { model: model }),
         React.createElement(StatusMessage, { model: model, variant: "header" }),
-        React.createElement(Tooltip, { title: "About" },
-            React.createElement(IconButton, { "aria-label": "About", onClick: () => {
-                    model.queueDialog(onClose => [AboutDialog, { onClose }]);
+        React.createElement(Tooltip, { title: "Mouse & keyboard help" },
+            React.createElement(IconButton, { "aria-label": "Mouse & keyboard help", onClick: () => {
+                    model.queueDialog(onClose => [HelpDialog, { model, onClose }]);
                 } },
                 React.createElement(Help, null)))));
 });

package/dist/components/header/Header.js.map

@@ -1 +1 @@
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package/dist/components/header/TreeSettingsMenu.d.ts

@@ -2,5 +2,5 @@ import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
 declare const TreeSettingsMenu: ({ model, }: {
     model: MsaViewModel;
-}) => React.JSX.Element;
+}) => React.JSX.Element | null;
 export default TreeSettingsMenu;

package/dist/components/header/TreeSettingsMenu.js

@@ -2,40 +2,9 @@ import React from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 import AccountTree from '@mui/icons-material/AccountTree';
 import { observer } from 'mobx-react';
-import { maxNeighborJoiningRows } from '../../constants.js';
 import { treeSettingsMenuItems } from './settingsMenuItems.js';
 const TreeSettingsMenu = observer(function ({ model, }) {
-    const { rows } = model;
-    const tooManyRows = rows.length > maxNeighborJoiningRows;
-    return (React.createElement(CascadingMenuButton, { "data-testid": "tree_settings_menu", tooltip: "Tree settings", closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: [
-            ...treeSettingsMenuItems(model),
-            ...(rows.length >= 2
-                ? [
-                    {
-                        label: 'Advanced',
-                        type: 'subMenu',
-                        subMenu: [
-                            {
-                                // the label shows the cap before a click would freeze the tab
-                                label: tooManyRows
-                                    ? `Calculate neighbor joining tree (over ${maxNeighborJoiningRows} rows, use FastTree)`
-                                    : 'Calculate neighbor joining tree (BLOSUM62)',
-                                disabled: tooManyRows,
-                                onClick: () => {
-                                    try {
-                                        model.calculateNeighborJoiningTreeFromMSA();
-                                    }
-                                    catch (e) {
-                                        console.error('Failed to calculate NJ tree:', e);
-                                        model.setError(e);
-                                    }
-                                },
-                            },
-                        ],
-                    },
-                ]
-                : []),
-        ] },
+    return model.noTree ? null : (React.createElement(CascadingMenuButton, { "data-testid": "tree_settings_menu", tooltip: "Tree settings", closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: treeSettingsMenuItems(model) },
         React.createElement(AccountTree, null)));
 });
 export default TreeSettingsMenu;

package/dist/components/header/TreeSettingsMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeSettingsMenu.js","sourceRoot":"","sources":["../../../src/components/header/TreeSettingsMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,qBAAqB,EAAE,MAAM,wBAAwB,CAAA;AAI9D,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,GAGN;IACC,OAAO,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAC3B,oBAAC,mBAAmB,mBACN,oBAAoB,EAChC,OAAO,EAAC,eAAe,EACvB,mBAAmB,EAAE,KAAK,EAC1B,YAAY,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,eAAe,EAAE,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,EACxD,SAAS,EAAE,qBAAqB,CAAC,KAAK,CAAC;QAEvC,oBAAC,WAAW,OAAG,CACK,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/header/ZoomControls.js

@@ -1,40 +1,12 @@
 import React from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import FitScreen from '@mui/icons-material/FitScreen';
+import RestartAlt from '@mui/icons-material/RestartAlt';
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
 import { IconButton, Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
-import { MouseScroll, MouseZoomBoth, MouseZoomHorizontal, MouseZoomVertical, } from './ScrollZoomIcons.js';
-const scrollMode = {
-    label: 'Scrolls the alignment',
-    Icon: MouseScroll,
-    helpText: 'Ctrl+wheel zooms both axes at the cursor.',
-};
-const wheelModes = [
-    scrollMode,
-    {
-        label: 'Zooms both axes',
-        axis: 'both',
-        Icon: MouseZoomBoth,
-        helpText: 'Hold shift to pan while the wheel zooms.',
-    },
-    {
-        label: 'Zooms columns only',
-        axis: 'horizontal',
-        Icon: MouseZoomHorizontal,
-        helpText: 'Holds the row height, so the labels and letters stay at their size while the alignment compresses.',
-    },
-    {
-        label: 'Zooms rows only',
-        axis: 'vertical',
-        Icon: MouseZoomVertical,
-        helpText: 'Holds the column width, so the alignment stays as wide while the rows grow or shrink.',
-    },
-];
 const ZoomControls = observer(function ZoomControls({ model, }) {
-    const { scrollZoom, scrollZoomAxis } = model;
-    const activeAxis = scrollZoom ? scrollZoomAxis : undefined;
-    const current = wheelModes.find(m => m.axis === activeAxis) ?? scrollMode;
     return (React.createElement(React.Fragment, null,
         React.createElement(Tooltip, { title: "Zoom in" },
             React.createElement(IconButton, { "aria-label": "Zoom in", onClick: () => {
@@ -46,23 +18,35 @@ const ZoomControls = observer(function ZoomControls({ model, }) {
                     model.zoomOut();
                 } },
                 React.createElement(ZoomOut, null))),
-        React.createElement(CascadingMenuButton, { "data-testid": "scroll_zoom_menu", tooltip: `Mouse wheel: ${current.label.toLowerCase()} (ctrl+wheel always zooms)`, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: [
-                { type: 'subHeader', label: 'Mouse wheel' },
-                ...wheelModes.map(({ label, axis, Icon, helpText }) => ({
-                    label,
-                    icon: Icon,
-                    helpText,
-                    type: 'radio',
-                    checked: current.label === label,
+        React.createElement(CascadingMenuButton, { "data-testid": "fit_menu", tooltip: "Fit or reset zoom", menuItems: [
+                {
+                    label: 'Fit to window',
                     onClick: () => {
-                        model.setScrollZoom(axis !== undefined);
-                        if (axis !== undefined) {
-                            model.setScrollZoomAxis(axis);
-                        }
+                        model.fit();
                     },
-                })),
+                },
+                {
+                    label: 'Fit horizontally',
+                    onClick: () => {
+                        model.fitHorizontally();
+                    },
+                },
+                {
+                    label: 'Fit vertically',
+                    onClick: () => {
+                        model.fitVertically();
+                    },
+                },
+                { type: 'divider' },
+                {
+                    label: 'Reset zoom',
+                    icon: RestartAlt,
+                    onClick: () => {
+                        model.resetZoom();
+                    },
+                },
             ] },
-            React.createElement(current.Icon, null))));
+            React.createElement(FitScreen, null))));
 });
 export default ZoomControls;
 //# sourceMappingURL=ZoomControls.js.map

package/dist/components/header/ZoomControls.js.map

@@ -1 +1 @@
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package/dist/components/header/settingsMenuItems.d.ts

@@ -1,4 +1,5 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { MenuItem } from '@jbrowse/core/ui/Menu';
+export declare function wheelSubMenu(model: MsaViewModel): MenuItem[];
 export declare function msaSettingsMenuItems(model: MsaViewModel): MenuItem[];
 export declare function treeSettingsMenuItems(model: MsaViewModel): MenuItem[];

package/dist/components/header/settingsMenuItems.js

@@ -1,4 +1,5 @@
 import { treeOrders } from '../../constants.js';
+import { MouseScroll, MouseZoomBoth, MouseZoomHorizontal, MouseZoomVertical, } from './ScrollZoomIcons.js';
 function radio(label, checked, onClick) {
     return { label, type: 'radio', checked, onClick };
 }
@@ -31,6 +32,44 @@ function tracksSubMenu(model) {
         model.toggleTrack(id);
     }));
 }
+const wheelModes = [
+    {
+        label: 'Scrolls the alignment',
+        icon: MouseScroll,
+        helpText: 'Ctrl+wheel zooms both axes at the cursor.',
+    },
+    {
+        label: 'Zooms both axes',
+        axis: 'both',
+        icon: MouseZoomBoth,
+        helpText: 'Hold shift to pan while the wheel zooms.',
+    },
+    {
+        label: 'Zooms columns only',
+        axis: 'horizontal',
+        icon: MouseZoomHorizontal,
+        helpText: 'Holds the row height, so the labels and letters stay at their size while the alignment compresses.',
+    },
+    {
+        label: 'Zooms rows only',
+        axis: 'vertical',
+        icon: MouseZoomVertical,
+        helpText: 'Holds the column width, so the alignment stays as wide while the rows grow or shrink.',
+    },
+];
+export function wheelSubMenu(model) {
+    const active = model.scrollZoom ? model.scrollZoomAxis : undefined;
+    return wheelModes.map(({ label, axis, icon, helpText }) => ({
+        ...radio(label, axis === active, () => {
+            model.setScrollZoom(axis !== undefined);
+            if (axis !== undefined) {
+                model.setScrollZoomAxis(axis);
+            }
+        }),
+        icon,
+        helpText,
+    }));
+}
 export function msaSettingsMenuItems(model) {
     const { drawMsaLetters, hideGaps, bgColor, showColumnStats } = model;
     return [
@@ -39,6 +78,11 @@ export function msaSettingsMenuItems(model) {
             type: 'subMenu',
             subMenu: tracksSubMenu(model),
         },
+        {
+            label: 'Mouse wheel',
+            type: 'subMenu',
+            subMenu: wheelSubMenu(model),
+        },
         { type: 'divider' },
         toggle('Show track values on hover', showColumnStats, arg => {
             model.setShowColumnStats(arg);
@@ -56,7 +100,7 @@ export function msaSettingsMenuItems(model) {
     ];
 }
 export function treeSettingsMenuItems(model) {
-    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawNodeLabels, drawLabels, showTreeOverview, treeOrder, treeRoot, rotated, } = model;
+    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview, treeOrder, treeRoot, rotated, } = model;
     return [
         {
             label: 'Order',
@@ -119,6 +163,9 @@ export function treeSettingsMenuItems(model) {
         toggle('Draw labels', drawLabels, arg => {
             model.setDrawLabels(arg);
         }),
+        toggle('Fit tree area to labels and tree', treeAreaWidth === undefined, arg => {
+            model.setTreeAreaWidth(arg ? undefined : model.effectiveTreeAreaWidth);
+        }),
     ];
 }
 //# sourceMappingURL=settingsMenuItems.js.map

package/dist/components/header/settingsMenuItems.js.map

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

@@ -1,3 +1,2 @@
 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/import/data/seq2.js

@@ -12,22 +12,5 @@ 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/import/data/seq2.js.map

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

package/dist/components/msa/MSACanvas.js

@@ -1,6 +1,7 @@
 import React, { useCallback, useRef } from 'react';
 import { observer } from 'mobx-react';
 import { useWheelScroll } from '../../useWheelScroll.js';
+import { alignmentAriaLabel } from '../controls.js';
 import Loading from './Loading.js';
 import MSACanvasBlock from './MSACanvasBlock.js';
 import { onMsaKey } from './msaKeys.js';
@@ -23,7 +24,7 @@ const MSACanvas = observer(function ({ model }) {
         onZoom,
         scrollZoom,
     });
-    return (React.createElement("div", { ref: ref, "data-testid": "msa_canvas", tabIndex: 0, "aria-label": "Alignment. Arrow keys scroll, shift pages, + and - zoom, Home and End jump to the first and last column. Shift-drag selects cells, and Escape clears the selection.", onKeyDown: event => {
+    return (React.createElement("div", { ref: ref, "data-testid": "msa_canvas", tabIndex: 0, "aria-label": alignmentAriaLabel, onKeyDown: event => {
             if (onMsaKey(model, event)) {
                 event.preventDefault();
             }

package/dist/components/msa/MSACanvas.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSACanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AACxD,OAAO,EAAE,kBAAkB,EAAE,MAAM,gBAAgB,CAAA;AACnD,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,EAAE,QAAQ,EAAE,MAAM,cAAc,CAAA;AAIvC,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EACJ,GAAG,EACH,aAAa,EACb,MAAM,EACN,cAAc,EACd,QAAQ,EACR,UAAU,EACV,OAAO,EACP,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,WAAmB,EAAE,OAAe,EAAE,OAAe,EAAE,EAAE;QACxD,KAAK,CAAC,SAAS,CAAC,WAAW,EAAE,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC,aAAa,CAAC,CAAA;IACrE,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,cAAc,CAAC;QAChD,GAAG;QACH,SAAS;QACT,SAAS;QACT,MAAM;QACN,UAAU;KACX,CAAC,CAAA;IAEF,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,iBAGI,YAAY,EACxB,QAAQ,EAAE,CAAC,gBACC,kBAAkB,EAC9B,SAAS,EAAE,KAAK,CAAC,EAAE;YACjB,IAAI,QAAQ,CAAC,KAAK,EAAE,KAAK,CAAC,EAAE,CAAC;gBAC3B,KAAK,CAAC,cAAc,EAAE,CAAA;YACxB,CAAC;QACH,CAAC,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,oEAAoE;YACpE,sEAAsE;YACtE,iBAAiB;YACjB,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;gBACnB,KAAK,CAAC,cAAc,EAAE,CAAA;gBACtB,GAAG,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAA;YAC7C,CAAC;iBAAM,CAAC;gBACN,WAAW,CAAC,KAAK,CAAC,CAAA;YACpB,CAAC;QACH,CAAC,EACD,SAAS,EAAE,SAAS,EACpB,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM;YACN,KAAK,EAAE,cAAc;YACrB,QAAQ,EAAE,QAAQ;SACnB,IAEA,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAGrC,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,SAAS,EAAE,aAAa,OAAO,OAAO,OAAO,KAAK;YAClD,UAAU,EAAE,WAAW;SACxB,IAEA,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAC1B,oBAAC,cAAc,IACb,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,EAAE,EAClB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,EAAE,EACX,OAAO,EAAE,EAAE,GACX,CACH,CAAC,CACE,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,OAAG,CACZ,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/components/msa/MSACanvasBlock.js

@@ -3,7 +3,7 @@ import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
-import { drawMsaRaster, rasterSupported } from './msaRaster.js';
+import { drawMsaRaster, rasterApplies } from './msaRaster.js';
 import { renderBoxFeatureCanvasBlock } from './renderBoxFeatureCanvasBlock.js';
 import { renderMSABlock } from './renderMSABlock.js';
 import { useMsaBlockMouse } from './useMsaBlockMouse.js';
@@ -23,10 +23,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
                 offsetY,
                 model,
             });
-            // the alignment background comes from zoom-independent raster tiles; the
-            // domain overlay paints its own boxes instead, and letter-color mode has
-            // no background to paint
-            const rasterTiles = !model.actuallyShowDomains && model.bgColor && rasterSupported();
+            const rasterTiles = rasterApplies(model);
             if (rasterTiles) {
                 drawMsaRaster({ ctx, model, theme, offsetX, offsetY });
             }

package/dist/components/msa/MSACanvasBlock.js.map

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