react-msaview 9.1.0 → 9.1.1

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

@@ -0,0 +1 @@
+{"version":3,"file":"metadataRecord.js","sourceRoot":"","sources":["../../../src/components/dialogs/metadataRecord.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAA;AAE1D,MAAM,aAAa,GAAG,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,CAAU,CAAA;AAE7D,SAAS,MAAM,CAAC,EAAU;IACxB,OAAO,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CACxB,2BACE,IAAI,EAAE,mCAAmC,EAAE,GAAG,EAC9C,MAAM,EAAC,QAAQ,EACf,GAAG,EAAC,YAAY,IAEf,EAAE,CACD,CACL,CAAC,CAAC,CAAC,CACF,EAAE,CACH,CAAA;AACH,CAAC;AAED,SAAS,eAAe,CAAC,OAAgC;IACvD,MAAM,OAAO,GAAG,OAAO,CAAC,EAAE,CAAA;IAC1B,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpD,OAAO,OAAO,CAAA;IAChB,CAAC;IACD,MAAM,OAAO,GAAG,aAAa,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;IACjE,MAAM,OAAO,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE;QAClC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QAC3B,OAAO,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,MAAM,CAAC,MAAM,KAAK,OAAO,CAAC,MAAM,CAAA;IAClE,CAAC,CAAC,CAAA;IACF,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,OAAO,OAAO,CAAA;IAChB,CAAC;IACD,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,CAC7B,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,CAC5B,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CACR,GAAG,KAAK,IAAI,IAAI,CAAE,aAAmC,CAAC,QAAQ,CAAC,GAAG,CAAC,CACtE,CACF,CAAA;IACD,MAAM,UAAU,GAAG,MAAM,CAAC,WAAW,CACnC,OAAO,CAAC,GAAG,CAAC,CAAC,MAAc,EAAE,CAAC,EAAE,EAAE,CAAC;QACjC,MAAM;QACN,MAAM,CAAC,WAAW,CAChB,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;YAChB,MAAM,KAAK,GAAI,OAAO,CAAC,GAAG,CAAc,CAAC,CAAC,CAAE,CAAA;YAC5C,OAAO;gBACL,oBAAoB,CAAC,GAAG,CAAC;gBACzB,GAAG,KAAK,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK;aACrC,CAAA;QACH,CAAC,CAAC,CACH;KACF,CAAC,CACH,CAAA;IACD,OAAO,EAAE,GAAG,IAAI,EAAE,UAAU,EAAE,UAAU,EAAE,CAAA;AAC5C,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,OAAgB;IAC3C,OAAO,OAAO,IAAI,OAAO,OAAO,KAAK,QAAQ;QAC3C,CAAC,CAAC,eAAe,CAAC,OAAkC,CAAC;QACrD,CAAC,CAAC,EAAE,CAAA;AACR,CAAC"}

package/dist/components/header/Header.d.ts

@@ -1,6 +1,10 @@
 import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
-declare const Header: ({ model }: {
+export interface ToolbarSlots {
+    toolbarStart?: React.ReactNode;
+    toolbarEnd?: React.ReactNode;
+}
+declare const Header: ({ model, toolbarStart, toolbarEnd, }: {
     model: MsaViewModel;
-}) => React.JSX.Element;
+} & ToolbarSlots) => React.JSX.Element;
 export default Header;

package/dist/components/header/Header.js

@@ -1,23 +1,19 @@
-import React, { lazy, useEffect } from 'react';
+import React, { useEffect } from 'react';
 import useMeasure from '@jbrowse/core/util/useMeasure';
-import Help from '@mui/icons-material/Help';
-import { IconButton, Tooltip } from '@mui/material';
+import Tune from '@mui/icons-material/Tune';
+import { AppBar, Button, IconButton, Toolbar, Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
 import StatusMessage from '../StatusMessage.js';
-import ColorSchemeMenu from './ColorSchemeMenu.js';
-import FileMenu from './FileMenu.js';
-import GappynessSlider from './GappynessSlider.js';
-import GoToBox from './GoToBox.js';
 import HeaderInfoArea from './HeaderInfoArea.js';
+import HiddenColumnsChip from './HiddenColumnsChip.js';
 import LoadWarnings from './LoadWarnings.js';
-import MSASettingsMenu from './MSASettingsMenu.js';
+import MenuBar from './MenuBar.js';
 import MultiAlignmentSelector from './MultiAlignmentSelector.js';
+import ScrollZoomCheckbox from './ScrollZoomCheckbox.js';
 import SelectionMenu from './SelectionMenu.js';
-import TreeSettingsMenu from './TreeSettingsMenu.js';
 import UnshareableDataWarning from './UnshareableDataWarning.js';
 import ZoomControls from './ZoomControls.js';
-const HelpDialog = lazy(() => import('../dialogs/HelpDialog.js'));
-const Header = observer(function ({ model }) {
+const Header = observer(function ({ model, toolbarStart, toolbarEnd, }) {
     const [ref, { height }] = useMeasure();
     useEffect(() => {
         model.setHeaderHeight(height ?? 0);
@@ -25,27 +21,29 @@ const Header = observer(function ({ model }) {
     useEffect(() => () => {
         model.setHeaderHeight(0);
     }, [model]);
-    return (React.createElement("div", { ref: ref, style: { display: 'flex', flexWrap: 'wrap' } },
-        React.createElement(FileMenu, { model: model }),
-        React.createElement(ColorSchemeMenu, { model: model }),
-        React.createElement(TreeSettingsMenu, { model: model }),
-        React.createElement(MSASettingsMenu, { model: model }),
-        React.createElement(ZoomControls, { model: model }),
-        React.createElement(GappynessSlider, { model: model }),
-        React.createElement(GoToBox, { model: model }),
-        React.createElement("div", { style: { paddingLeft: 20, margin: 'auto' } },
-            React.createElement(MultiAlignmentSelector, { model: model })),
-        React.createElement("div", { style: { flex: '1 1 0', minWidth: 0, display: 'flex' } },
-            React.createElement(SelectionMenu, { model: model }),
-            React.createElement(HeaderInfoArea, { model: model })),
-        React.createElement(LoadWarnings, { model: model }),
-        React.createElement(UnshareableDataWarning, { model: model }),
-        React.createElement(StatusMessage, { model: model, variant: "header" }),
-        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)))));
+    return (React.createElement(AppBar, { ref: ref, position: "static", color: "default", elevation: 0, sx: { borderBottom: 1, borderColor: 'divider' } },
+        React.createElement(Toolbar, { variant: "dense", disableGutters: true, sx: { minHeight: 40, flexWrap: 'wrap', px: 0.5 } },
+            toolbarStart,
+            React.createElement(MenuBar, { model: model }),
+            model.embeddedMode ? (React.createElement(Tooltip, { title: "Settings" },
+                React.createElement(IconButton, { "data-testid": "settings_button", "aria-label": "Settings", color: model.settingsOpen ? 'primary' : 'inherit', onClick: () => {
+                        model.setSettingsOpen(!model.settingsOpen);
+                    } },
+                    React.createElement(Tune, null)))) : (React.createElement(Button, { "data-testid": "settings_button", size: "small", startIcon: React.createElement(Tune, null), color: model.settingsOpen ? 'primary' : 'inherit', variant: model.settingsOpen ? 'outlined' : 'text', onClick: () => {
+                    model.setSettingsOpen(!model.settingsOpen);
+                }, sx: { mx: 0.5, flexShrink: 0 } }, "Settings")),
+            React.createElement(ZoomControls, { model: model }),
+            React.createElement(ScrollZoomCheckbox, { model: model }),
+            React.createElement(HiddenColumnsChip, { model: model }),
+            React.createElement("div", { style: { paddingLeft: 20, margin: 'auto' } },
+                React.createElement(MultiAlignmentSelector, { model: model })),
+            React.createElement("div", { style: { flex: '1 1 0', minWidth: 0, display: 'flex' } },
+                React.createElement(SelectionMenu, { model: model }),
+                React.createElement(HeaderInfoArea, { model: model })),
+            React.createElement(LoadWarnings, { model: model }),
+            React.createElement(UnshareableDataWarning, { model: model }),
+            React.createElement(StatusMessage, { model: model, variant: "header" }),
+            toolbarEnd)));
 });
 export default Header;
 //# sourceMappingURL=Header.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAExC,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAC5E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,aAAa,MAAM,qBAAsB,CAAA;AAChD,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,iBAAiB,MAAM,wBAAyB,CAAA;AACvD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,sBAAsB,MAAM,6BAA8B,CAAA;AACjE,OAAO,kBAAkB,MAAM,yBAA0B,CAAA;AACzD,OAAO,aAAa,MAAM,oBAAqB,CAAA;AAC/C,OAAO,sBAAsB,MAAM,6BAA8B,CAAA;AACjE,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAS7C,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAChC,KAAK,EACL,YAAY,EACZ,UAAU,GAC6B;IACvC,MAAM,CAAC,GAAG,EAAE,EAAE,MAAM,EAAE,CAAC,GAAG,UAAU,EAAE,CAAA;IACtC,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,eAAe,CAAC,MAAM,IAAI,CAAC,CAAC,CAAA;IACpC,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACnB,SAAS,CACP,GAAG,EAAE,CAAC,GAAG,EAAE;QACT,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,OAAO,CACL,oBAAC,MAAM,IACL,GAAG,EAAE,GAAG,EACR,QAAQ,EAAC,QAAQ,EACjB,KAAK,EAAC,SAAS,EACf,SAAS,EAAE,CAAC,EACZ,EAAE,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,WAAW,EAAE,SAAS,EAAE;QAE/C,oBAAC,OAAO,IACN,OAAO,EAAC,OAAO,EACf,cAAc,QACd,EAAE,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,EAAE;YAE/C,YAAY;YACb,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;YACxB,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,CACpB,oBAAC,OAAO,IAAC,KAAK,EAAC,UAAU;gBACvB,oBAAC,UAAU,mBACG,iBAAiB,gBAClB,UAAU,EACrB,KAAK,EAAE,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EACjD,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;oBAC5C,CAAC;oBAED,oBAAC,IAAI,OAAG,CACG,CACL,CACX,CAAC,CAAC,CAAC,CACF,oBAAC,MAAM,mBACO,iBAAiB,EAC7B,IAAI,EAAC,OAAO,EACZ,SAAS,EAAE,oBAAC,IAAI,OAAG,EACnB,KAAK,EAAE,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EACjD,OAAO,EAAE,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,MAAM,EACjD,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,eAAe,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;gBAC5C,CAAC,EACD,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,EAAE,UAAU,EAAE,CAAC,EAAE,eAGvB,CACV;YACD,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;YAC9B,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI;YACpC,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI;YACnC,6BAAK,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;gBAC7C,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC;YAGN,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,OAAO,EAAE,MAAM,EAAE;gBACzD,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,GAAI;gBAC/B,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CAC5B;YACN,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;YAC9B,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;YACxC,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAC,QAAQ,GAAG;YAC/C,UAAU,CACH,CACH,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,MAAM,CAAA"}

package/dist/components/header/{TreeSettingsMenu.d.ts → HiddenColumnsChip.d.ts}

@@ -1,6 +1,6 @@
 import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
-declare const TreeSettingsMenu: ({ model, }: {
+declare const HiddenColumnsChip: ({ model, }: {
     model: MsaViewModel;
 }) => React.JSX.Element | null;
-export default TreeSettingsMenu;
+export default HiddenColumnsChip;

package/dist/components/header/HiddenColumnsChip.js

@@ -0,0 +1,15 @@
+import React, { lazy } from 'react';
+import { Chip, Tooltip } from '@mui/material';
+import { observer } from 'mobx-react';
+const GapThresholdDialog = lazy(() => import('../dialogs/GapThresholdDialog.js'));
+const HiddenColumnsChip = observer(function ({ model, }) {
+    const n = model.blanks.length;
+    return n > 0 ? (React.createElement(Tooltip, { title: `Hiding columns with ≥${model.allowedGappyness}% gaps. Click to change the threshold, × to show every column` },
+        React.createElement(Chip, { "data-testid": "hidden_columns_chip", size: "small", variant: "outlined", label: `${n.toLocaleString('en-US')} gappy column${n === 1 ? '' : 's'} hidden`, style: { margin: 'auto 8px', flexShrink: 0 }, onClick: () => {
+                model.queueDialog(onClose => [GapThresholdDialog, { model, onClose }]);
+            }, onDelete: () => {
+                model.setHideGaps(false);
+            } }))) : null;
+});
+export default HiddenColumnsChip;
+//# sourceMappingURL=HiddenColumnsChip.js.map

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

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

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

package/dist/components/header/MenuBar.js

@@ -0,0 +1,33 @@
+import React from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import Build from '@mui/icons-material/Build';
+import Help from '@mui/icons-material/Help';
+import InsertDriveFile from '@mui/icons-material/InsertDriveFile';
+import Visibility from '@mui/icons-material/Visibility';
+import { Tooltip } from '@mui/material';
+import { observer } from 'mobx-react';
+import { fileMenuItems, helpMenuItems, toolsMenuItems, viewMenuItems, } from './menuBarItems.js';
+// CascadingMenuButton renders an IconButton on every core a host may ship, so
+// these styles give it the look of a small text Button
+const menuButtonSx = {
+    borderRadius: 1,
+    typography: 'button',
+    color: 'text.primary',
+    px: 1,
+    py: 0.5,
+};
+const menus = [
+    ['File', fileMenuItems, React.createElement(InsertDriveFile, { key: "file" })],
+    ['View', viewMenuItems, React.createElement(Visibility, { key: "view" })],
+    ['Tools', toolsMenuItems, React.createElement(Build, { key: "tools" })],
+    ['Help', helpMenuItems, React.createElement(Help, { key: "help" })],
+];
+const MenuBar = observer(function ({ model }) {
+    const { embeddedMode } = model;
+    return menus.map(([name, items, icon]) => {
+        const button = (React.createElement(CascadingMenuButton, { key: name, "data-testid": `${name.toLowerCase()}_menu`, "aria-label": name, menuItems: items(model), sx: menuButtonSx }, embeddedMode ? icon : name));
+        return embeddedMode ? (React.createElement(Tooltip, { key: name, title: name }, button)) : (button);
+    });
+});
+export default MenuBar;
+//# sourceMappingURL=MenuBar.js.map

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

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

@@ -0,0 +1,7 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+export declare const scrollZoomLabel = "Zoom on scroll";
+declare const ScrollZoomCheckbox: ({ model, }: {
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default ScrollZoomCheckbox;

package/dist/components/header/ScrollZoomCheckbox.js

@@ -0,0 +1,19 @@
+import React from 'react';
+import { Checkbox, FormControlLabel, Tooltip } from '@mui/material';
+import { observer } from 'mobx-react';
+// the label and the control jbrowse-components' ScrollZoomToggle uses, kept
+// local because a host's older core lacks that export
+export const scrollZoomLabel = 'Zoom on scroll';
+const scrollZoomHelp = 'The mouse wheel zooms the alignment instead of scrolling it; shift+scroll still scrolls. ctrl+scroll (⌘+scroll on a Mac) zooms either way.';
+const ScrollZoomCheckbox = observer(function ({ model, }) {
+    return (React.createElement(Tooltip, { title: scrollZoomHelp, describeChild: true },
+        React.createElement(FormControlLabel, { "data-testid": "scroll-zoom-toggle", style: {
+                marginLeft: 4,
+                marginRight: model.embeddedMode ? 0 : 8,
+                whiteSpace: 'nowrap',
+            }, control: React.createElement(Checkbox, { size: "small", checked: model.scrollZoom, onChange: () => {
+                    model.setScrollZoom(!model.scrollZoom);
+                }, style: { padding: 6 } }), label: model.embeddedMode ? '' : scrollZoomLabel, slotProps: { typography: { variant: 'body2' } } })));
+});
+export default ScrollZoomCheckbox;
+//# sourceMappingURL=ScrollZoomCheckbox.js.map

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

@@ -0,0 +1 @@
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package/dist/components/header/ZoomControls.js

@@ -1,5 +1,4 @@
 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';
@@ -18,35 +17,16 @@ const ZoomControls = observer(function ZoomControls({ model, }) {
                     model.zoomOut();
                 } },
                 React.createElement(ZoomOut, null))),
-        React.createElement(CascadingMenuButton, { "data-testid": "fit_menu", tooltip: "Fit or reset zoom", menuItems: [
-                {
-                    label: 'Fit to window',
-                    onClick: () => {
-                        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(FitScreen, null))));
+        React.createElement(Tooltip, { title: "Fit the whole alignment in the window" },
+            React.createElement(IconButton, { "aria-label": "Fit to window", onClick: () => {
+                    model.fit();
+                } },
+                React.createElement(FitScreen, null))),
+        React.createElement(Tooltip, { title: "Reset zoom to the default cell size (0)" },
+            React.createElement(IconButton, { "aria-label": "Reset zoom", onClick: () => {
+                    model.resetZoom();
+                } },
+                React.createElement(RestartAlt, 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/colorSchemeMenuItems.d.ts

@@ -0,0 +1,4 @@
+import type { MsaViewModel } from '../../model.ts';
+import type { MenuItem } from '@jbrowse/core/ui/Menu';
+export declare const catalogedSchemeNames: string[];
+export declare function colorSchemeMenuItems(model: MsaViewModel): MenuItem[];

package/dist/components/header/colorSchemeMenuItems.js

@@ -0,0 +1,106 @@
+const schemes = [
+    { name: 'maeditor', label: 'MAEditor', alphabet: 'protein', featured: true },
+    {
+        name: 'clustalx_protein',
+        label: 'Clustal X',
+        alphabet: 'protein',
+        featured: true,
+    },
+    {
+        name: 'clustalx_protein_dynamic',
+        label: 'Clustal X, by column conservation',
+        alphabet: 'protein',
+        featured: true,
+    },
+    {
+        name: 'blosum62_dynamic',
+        label: 'BLOSUM62 similarity',
+        alphabet: 'protein',
+        featured: true,
+    },
+    {
+        name: 'jalview_hydrophobicity',
+        label: 'Hydrophobicity',
+        alphabet: 'protein',
+        featured: true,
+    },
+    {
+        name: 'nucleotide',
+        label: 'Nucleotide',
+        alphabet: 'nucleotide',
+        featured: true,
+    },
+    {
+        name: 'rainbow_dna',
+        label: 'Rainbow',
+        alphabet: 'nucleotide',
+        featured: true,
+    },
+    {
+        name: 'percent_identity_dynamic',
+        label: 'Percent identity',
+        alphabet: 'any',
+        featured: true,
+    },
+    { name: 'none', label: 'None', alphabet: 'any', featured: true },
+    { name: 'clustal', label: 'Clustal', alphabet: 'protein' },
+    { name: 'lesk', label: 'Lesk', alphabet: 'protein' },
+    { name: 'flower', label: 'Flower', alphabet: 'protein' },
+    { name: 'cinema', label: 'Cinema', alphabet: 'protein' },
+    { name: 'jalview_zappo', label: 'Zappo', alphabet: 'protein' },
+    { name: 'jalview_taylor', label: 'Taylor', alphabet: 'protein' },
+    { name: 'jalview_buried', label: 'Buried index', alphabet: 'protein' },
+    { name: 'jalview_prophelix', label: 'Helix propensity', alphabet: 'protein' },
+    {
+        name: 'jalview_propstrand',
+        label: 'Strand propensity',
+        alphabet: 'protein',
+    },
+    { name: 'jalview_propturn', label: 'Turn propensity', alphabet: 'protein' },
+    { name: 'clustalx_dna', label: 'Clustal X (DNA)', alphabet: 'nucleotide' },
+    { name: 'jbrowse_dna', label: 'JBrowse (DNA)', alphabet: 'nucleotide' },
+];
+export const catalogedSchemeNames = schemes.map(s => s.name);
+// While a `customColorScheme` map is set, a checked Custom entry stands for it
+// and no named scheme is checked. Picking a named scheme clears the map. The
+// active scheme always shows at the top level.
+export function colorSchemeMenuItems(model) {
+    const { colorSchemeName, customColorScheme, sequenceType } = model;
+    const alphabet = sequenceType === 'amino' ? 'protein' : 'nucleotide';
+    function radio(entry) {
+        return {
+            label: entry.label,
+            type: 'radio',
+            checked: !customColorScheme && colorSchemeName === entry.name,
+            onClick: () => {
+                model.setColorSchemeName(entry.name);
+                // a scheme picked while the domains fill the cells would color
+                // nothing, so the pick hands the cells back to the residues
+                if (model.cellFill === 'domain') {
+                    model.setCellFill('residue');
+                }
+            },
+        };
+    }
+    const top = (e) => (e.featured && (e.alphabet === 'any' || e.alphabet === alphabet)) ||
+        (!customColorScheme && e.name === colorSchemeName);
+    return [
+        ...(customColorScheme
+            ? [
+                {
+                    label: 'Custom',
+                    type: 'radio',
+                    checked: true,
+                    onClick: () => { },
+                },
+            ]
+            : []),
+        ...schemes.filter(top).map(radio),
+        {
+            label: 'More schemes',
+            type: 'subMenu',
+            subMenu: schemes.filter(e => !top(e)).map(radio),
+        },
+    ];
+}
+//# sourceMappingURL=colorSchemeMenuItems.js.map

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

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

@@ -1,31 +1,4 @@
 import type { MsaViewModel } from '../../model.ts';
-export declare function getAnnotationsMenu({ model }: {
-    model: MsaViewModel;
-}): ({
-    label: string;
-    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-        muiName: string;
-    };
-    onClick: () => void;
-    checked?: undefined;
-    type?: undefined;
-    disabled?: undefined;
-} | {
-    label: string;
-    disabled: boolean;
-    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-        muiName: string;
-    };
-    checked: boolean;
-    type: 'checkbox';
-    onClick: () => void;
-} | {
-    checked?: undefined;
-    type?: undefined;
-    label: string;
-    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-        muiName: string;
-    };
-    disabled: boolean;
-    onClick: () => void;
-})[];
+import type { MenuItem } from '@jbrowse/core/ui/Menu';
+export declare function openAnnotationFileItem(model: MsaViewModel): MenuItem;
+export declare function annotationsSubMenu(model: MsaViewModel): MenuItem[];

package/dist/components/header/getAnnotationsMenu.js

@@ -1,73 +1,67 @@
 import { lazy } from 'react';
-import FilterAlt from '@mui/icons-material/FilterAlt';
-import FolderOpen from '@mui/icons-material/FolderOpen';
-import MenuBook from '@mui/icons-material/MenuBook';
-import Sort from '@mui/icons-material/Sort';
-import Visibility from '@mui/icons-material/Visibility';
 const FeatureFilterDialog = lazy(() => import('../dialogs/FeatureDialog.js'));
 const AnnotationFileDialog = lazy(() => import('../dialogs/AnnotationFileDialog.js'));
-const domainsTutorial = 'https://gmod.org/JBrowseMSA/tutorials/protein_family';
-export function getAnnotationsMenu({ model }) {
-    const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model;
-    const noneLoaded = noDomains ? ' (none loaded)' : '';
-    return [
-        {
-            label: 'Open annotation file...',
-            icon: FolderOpen,
-            onClick: () => {
-                model.queueDialog(handleClose => [
-                    AnnotationFileDialog,
-                    {
-                        handleClose,
-                        model,
-                    },
-                ]);
-            },
-        },
-        // `react-msaview-cli interpro` reads InterPro's precomputed matches in
-        // seconds, and `interproscan` covers rows InterPro has not seen; this links
-        // the tutorial for both
-        {
-            label: 'How to get a domain file...',
-            icon: MenuBook,
-            onClick: () => {
-                window.open(domainsTutorial, '_blank', 'noopener,noreferrer');
-            },
+export function openAnnotationFileItem(model) {
+    return {
+        label: 'Open annotation file…',
+        onClick: () => {
+            model.queueDialog(handleClose => [
+                AnnotationFileDialog,
+                { handleClose, model },
+            ]);
         },
+    };
+}
+export function annotationsSubMenu(model) {
+    const { showDomains, actuallyShowDomains, subFeatureRows } = model;
+    return [
         {
-            label: `Show annotations${noneLoaded}`,
-            disabled: noDomains,
-            icon: Visibility,
-            checked: actuallyShowDomains,
+            label: 'Show annotations',
             type: 'checkbox',
+            checked: actuallyShowDomains,
             onClick: () => {
                 model.setShowDomains(!showDomains);
             },
         },
         {
-            label: `Use sub-row layout${noneLoaded}`,
-            disabled: noDomains,
-            checked: actuallyShowDomains ? subFeatureRows : false,
-            icon: Sort,
+            label: 'Sub-row layout',
             type: 'checkbox',
+            disabled: !actuallyShowDomains,
+            checked: actuallyShowDomains && subFeatureRows,
             onClick: () => {
                 model.setSubFeatureRows(!subFeatureRows);
             },
         },
-        {
-            label: `Filter annotations${noneLoaded}`,
-            icon: FilterAlt,
-            disabled: noDomains,
-            onClick: () => {
-                model.queueDialog(onClose => [
-                    FeatureFilterDialog,
-                    {
-                        onClose,
-                        model,
-                    },
-                ]);
-            },
-        },
+        ...typeItems(model),
     ];
 }
+// up to this many types list inline, one checkbox each; past it the filter
+// dialog, which searches and counts them, takes over
+const inlineTypes = 12;
+function typeItems(model) {
+    const types = [...model.annotationTypes.values()];
+    return types.length <= inlineTypes
+        ? [
+            { type: 'subHeader', label: 'Types' },
+            ...types.map(({ accession, name }) => ({
+                label: name || accession,
+                type: 'checkbox',
+                checked: !model.featureOff(accession),
+                onClick: () => {
+                    model.setFilter(accession, model.featureOff(accession));
+                },
+            })),
+        ]
+        : [
+            {
+                label: 'Filter annotations…',
+                onClick: () => {
+                    model.queueDialog(onClose => [
+                        FeatureFilterDialog,
+                        { onClose, model },
+                    ]);
+                },
+            },
+        ];
+}
 //# sourceMappingURL=getAnnotationsMenu.js.map

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

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package/dist/components/header/menuBarItems.d.ts

@@ -0,0 +1,11 @@
+import type { MsaViewModel } from '../../model.ts';
+import type { MenuItem } from '@jbrowse/core/ui/Menu';
+export declare function fileMenuItems(model: MsaViewModel): MenuItem[];
+export declare function gapsSubMenu(model: MsaViewModel): MenuItem[];
+export declare function treeSubMenu(model: MsaViewModel): MenuItem[];
+export declare function viewMenuItems(model: MsaViewModel): MenuItem[];
+export declare function trackSettingsItems(model: MsaViewModel): MenuItem[];
+export declare function alignmentSettingsItems(model: MsaViewModel): MenuItem[];
+export declare function colorSettingsItems(model: MsaViewModel): MenuItem[];
+export declare function toolsMenuItems(model: MsaViewModel): MenuItem[];
+export declare function helpMenuItems(model: MsaViewModel): MenuItem[];