react-msaview 4.4.0 → 4.4.1

package/dist/colorSchemes.js

@@ -1,7 +1,7 @@
 import { blue, green, orange, red } from '@mui/material/colors';
 import { colord, extend } from 'colord';
 import namesPlugin from 'colord/plugins/names';
-import { transform } from './util';
+import { isBlank, transform } from './util';
 extend([namesPlugin]);
 const colorSchemes = {
     none: {},
@@ -443,7 +443,7 @@ export function getPercentIdentityColor(stats, total, model, row, col) {
     let ent = 0;
     let letter = '';
     for (const entry of entries) {
-        if (entry[1] > ent && entry[0] !== '-') {
+        if (entry[1] > ent && !isBlank(entry[0])) {
             letter = entry[0];
             ent = entry[1];
         }

package/dist/colorSchemes.js.map

@@ -1 +1 @@
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package/dist/components/VerticalScrollbar.js

@@ -1,6 +1,6 @@
 import React, { useEffect, useRef, useState } from 'react';
+import { clamp } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import { clamp } from '../util';
 const VerticalScrollbar = observer(({ model }) => {
     const { msaAreaHeight, scrollY, totalHeight } = model;
     const [hovered, setHovered] = useState(false);
@@ -18,7 +18,7 @@ const VerticalScrollbar = observer(({ model }) => {
                 if (!scheduled.current) {
                     scheduled.current = true;
                     window.requestAnimationFrame(() => {
-                        model.setScrollY(clamp(-totalHeight, mouseDown.scrollY - (event.clientY - mouseDown.clientY) / unit, 0));
+                        model.setScrollY(clamp(mouseDown.scrollY - (event.clientY - mouseDown.clientY) / unit, -totalHeight, 0));
                         scheduled.current = false;
                     });
                 }

package/dist/components/VerticalScrollbar.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VerticalScrollbar.js","sourceRoot":"","sources":["../../src/components/VerticalScrollbar.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE1D,OAAO,EAAE,KAAK,EAAE,MAAM,oBAAoB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,iBAAiB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACxE,MAAM,EAAE,aAAa,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACrD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC/B,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAGtC,CAAA;IACJ,MAAM,IAAI,GAAG,yBAAyB,CAAA;IACtC,MAAM,IAAI,GAAG,aAAa,GAAG,WAAW,CAAA;IACxC,MAAM,GAAG,GAAG,CAAC,OAAO,CAAA;IACpB,MAAM,MAAM,GAAG,GAAG,GAAG,aAAa,CAAA;IAClC,MAAM,CAAC,GAAG,GAAG,GAAG,IAAI,CAAA;IACpB,MAAM,CAAC,GAAG,MAAM,GAAG,IAAI,CAAA;IACvB,SAAS,CAAC,GAAG,EAAE;QACb,SAAS,EAAE,CAAC,KAAiB;YAC3B,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;oBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;oBACxB,MAAM,CAAC,qBAAqB,CAAC,GAAG,EAAE;wBAChC,KAAK,CAAC,UAAU,CACd,KAAK,CACH,SAAS,CAAC,OAAO,GAAG,CAAC,KAAK,CAAC,OAAO,GAAG,SAAS,CAAC,OAAO,CAAC,GAAG,IAAI,EAC9D,CAAC,WAAW,EACZ,CAAC,CACF,CACF,CAAA;wBACD,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;oBAC3B,CAAC,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QACD,SAAS,GAAG;YACV,YAAY,CAAC,SAAS,CAAC,CAAA;QACzB,CAAC;QACD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;YAC5B,QAAQ,CAAC,gBAAgB,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;YAC1C,QAAQ,CAAC,gBAAgB,CAAC,SAAS,EAAE,GAAG,CAAC,CAAA;YACzC,OAAO,GAAG,EAAE;gBACV,QAAQ,CAAC,mBAAmB,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;gBAC7C,QAAQ,CAAC,mBAAmB,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;YAChD,CAAC,CAAA;QACH,CAAC;IACH,CAAC,EAAE,CAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,SAAS,CAAC,CAAC,CAAA;IACzC,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,aAAa;YACrB,UAAU,EAAE,gBAAgB;YAC5B,SAAS,EAAE,gBAAgB;YAC3B,SAAS,EAAE,YAAY;SACxB;QAED,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACnB,IAAI,EAAE,CAAC;gBACP,UAAU,EAAE,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,IAAI;gBACnD,MAAM,EAAE,SAAS;gBACjB,SAAS,EAAE,YAAY;gBACvB,KAAK,EAAE,EAAE;gBACT,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBAC3B,MAAM,EAAE,GAAG;aACZ,EACD,WAAW,EAAE,GAAG,EAAE;gBAChB,UAAU,CAAC,IAAI,CAAC,CAAA;YAClB,CAAC,EACD,UAAU,EAAE,GAAG,EAAE;gBACf,UAAU,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,YAAY,CAAC;oBACX,OAAO,EAAE,KAAK,CAAC,OAAO;oBACtB,OAAO,EAAE,KAAK,CAAC,OAAO;iBACvB,CAAC,CAAA;YACJ,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,iBAAiB,CAAA"}

package/dist/components/header/{SettingsMenu.d.ts → ColorMenu.d.ts}

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

package/dist/components/header/ColorMenu.js

@@ -0,0 +1,19 @@
+import React from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import Palette from '@mui/icons-material/Palette';
+import { observer } from 'mobx-react';
+import colorSchemes from '../../colorSchemes';
+const ColorMenu = observer(({ model }) => {
+    const { colorSchemeName } = model;
+    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, menuItems: Object.keys(colorSchemes).map(option => ({
+            label: option,
+            type: 'radio',
+            checked: colorSchemeName === option,
+            onClick: () => {
+                model.setColorSchemeName(option);
+            },
+        })) },
+        React.createElement(Palette, null)));
+});
+export default ColorMenu;
+//# sourceMappingURL=ColorMenu.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ColorMenu.js","sourceRoot":"","sources":["../../../src/components/header/ColorMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,OAAO,MAAM,6BAA6B,CAAA;AACjD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,YAAY,MAAM,oBAAoB,CAAA;AAI7C,MAAM,SAAS,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAChE,MAAM,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACjC,OAAO,CACL,oBAAC,mBAAmB,IAClB,mBAAmB,EAAE,KAAK,EAC1B,SAAS,EAAE,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CACtC,MAAM,CAAC,EAAE,CACP,CAAC;YACC,KAAK,EAAE,MAAM;YACb,IAAI,EAAE,OAAO;YACb,OAAO,EAAE,eAAe,KAAK,MAAM;YACnC,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;YAClC,CAAC;SACF,CAAU,CACd;QAED,oBAAC,OAAO,OAAG,CACS,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/components/header/Header.js

@@ -3,11 +3,13 @@ import useMeasure from '@jbrowse/core/util/useMeasure';
 import Help from '@mui/icons-material/Help';
 import { IconButton } from '@mui/material';
 import { observer } from 'mobx-react';
+import ColorMenu from './ColorMenu';
 import HeaderInfoArea from './HeaderInfoArea';
 import HeaderMenu from './HeaderMenu';
 import HeaderStatusArea from './HeaderStatusArea';
+import MSAMenu from './MSAMenu';
 import MultiAlignmentSelector from './MultiAlignmentSelector';
-import SettingsMenu from './SettingsMenu';
+import TreeMenu from './TreeMenu';
 import ZoomControls from './ZoomControls';
 import ZoomMenu from './ZoomMenu';
 import ZoomStar from './ZoomStar';
@@ -19,7 +21,9 @@ const Header = observer(function ({ model }) {
     }, [model, height]);
     return (React.createElement("div", { ref: ref, style: { display: 'flex' } },
         React.createElement(HeaderMenu, { model: model }),
-        React.createElement(SettingsMenu, { model: model }),
+        React.createElement(ColorMenu, { model: model }),
+        React.createElement(TreeMenu, { model: model }),
+        React.createElement(MSAMenu, { model: model }),
         React.createElement(ZoomControls, { model: model }),
         model.showZoomStar ? React.createElement(ZoomStar, { model: model }) : null,
         React.createElement(ZoomMenu, { model: model }),

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

@@ -1 +1 @@
-{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAIjC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC,CAAA;AAEhE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,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,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QACvC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI;QAC5B,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC7B,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QACvD,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;YAC5B,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;YAC1D,CAAC;YAED,oBAAC,IAAI,OAAG,CACG,CACT,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,MAAM;IACb,OAAO,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAAI,CAAA;AACpC,CAAC;AAED,eAAe,MAAM,CAAA"}
+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,OAAO,MAAM,WAAW,CAAA;AAC/B,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAIjC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC,CAAA;AAEhE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,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,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QACvC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI;QAC5B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC7B,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QACvD,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;YAC5B,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;YAC1D,CAAC;YAED,oBAAC,IAAI,OAAG,CACG,CACT,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,MAAM;IACb,OAAO,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAAI,CAAA;AACpC,CAAC;AAED,eAAe,MAAM,CAAA"}

package/dist/components/header/HeaderInfoArea.js

@@ -14,8 +14,9 @@ const HeaderInfoArea = observer(function ({ model }) {
     return mouseOverRowName && mouseCol !== undefined ? (React.createElement(Typography, { className: classes.margin },
         mouseOverRowName,
         ":",
-        model.mouseOverCoordToGapRemovedRowCoord(mouseOverRowName, mouseCol),
-        " (",
+        model.mouseOverCoordToGapRemovedRowCoordOneBased(mouseOverRowName, mouseCol),
+        ' ',
+        "(",
         model.mouseOverCoordToRowLetter(mouseOverRowName, mouseCol),
         ")")) : null;
 });

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

@@ -1 +1 @@
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+{"version":3,"file":"HeaderInfoArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderInfoArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC1E,MAAM,EAAE,gBAAgB,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,gBAAgB,IAAI,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,CAClD,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QAClC,gBAAgB;;QAChB,KAAK,CAAC,0CAA0C,CAC/C,gBAAgB,EAChB,QAAQ,CACT;QAAE,GAAG;;QACJ,KAAK,CAAC,yBAAyB,CAAC,gBAAgB,EAAE,QAAQ,CAAC;YAClD,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/header/HeaderMenu.js

@@ -1,28 +1,25 @@
 import React, { lazy } from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import AccountTreeIcon from '@mui/icons-material/AccountTree';
 import Assignment from '@mui/icons-material/Assignment';
 import FilterAlt from '@mui/icons-material/FilterAlt';
 import FolderOpen from '@mui/icons-material/FolderOpen';
-import GridOn from '@mui/icons-material/GridOn';
 import List from '@mui/icons-material/List';
 import MoreVert from '@mui/icons-material/Menu';
 import PhotoCamera from '@mui/icons-material/PhotoCamera';
 import Search from '@mui/icons-material/Search';
-import Settings from '@mui/icons-material/Settings';
 import Sort from '@mui/icons-material/Sort';
 import Visibility from '@mui/icons-material/Visibility';
 import { observer } from 'mobx-react';
 // lazies
-const SettingsDialog = lazy(() => import('../dialogs/SettingsDialog'));
 const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog'));
 const TracklistDialog = lazy(() => import('../dialogs/TracklistDialog'));
 const ExportSVGDialog = lazy(() => import('../dialogs/ExportSVGDialog'));
 const FeatureFilterDialog = lazy(() => import('../dialogs/FeatureDialog'));
+const SettingsDialog = lazy(() => import('../dialogs/SettingsDialog'));
 const UserProvidedDomainsDialog = lazy(() => import('../dialogs/UserProvidedDomainsDialog'));
 const InterProScanDialog = lazy(() => import('../dialogs/InterProScanDialog'));
 const HeaderMenu = observer(({ model }) => {
-    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, showDomains, actuallyShowDomains, subFeatureRows, drawLabels, treeWidthMatchesArea, noDomains, noTree, } = model;
+    const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model;
     return (React.createElement(CascadingMenuButton, { menuItems: [
             {
                 label: 'Return to import form',
@@ -31,97 +28,6 @@ const HeaderMenu = observer(({ model }) => {
                     model.reset();
                 },
             },
-            {
-                icon: Settings,
-                label: 'Settings',
-                type: 'subMenu',
-                subMenu: [
-                    {
-                        label: 'Tree settings',
-                        type: 'subMenu',
-                        icon: AccountTreeIcon,
-                        subMenu: [
-                            {
-                                label: 'Show branch length',
-                                type: 'checkbox',
-                                checked: showBranchLen,
-                                onClick: () => {
-                                    model.setShowBranchLen(!showBranchLen);
-                                },
-                            },
-                            {
-                                label: 'Show tree',
-                                type: 'checkbox',
-                                checked: drawTree,
-                                onClick: () => {
-                                    model.setDrawTree(!drawTree);
-                                },
-                            },
-                            {
-                                label: 'Draw clickable bubbles on tree branches',
-                                type: 'checkbox',
-                                checked: drawNodeBubbles,
-                                onClick: () => {
-                                    model.setDrawNodeBubbles(!drawNodeBubbles);
-                                },
-                            },
-                            {
-                                label: 'Tree labels align right',
-                                type: 'checkbox',
-                                checked: labelsAlignRight,
-                                onClick: () => {
-                                    model.setLabelsAlignRight(!labelsAlignRight);
-                                },
-                            },
-                            {
-                                label: 'Draw labels',
-                                type: 'checkbox',
-                                checked: drawLabels,
-                                onClick: () => {
-                                    model.setDrawLabels(!drawLabels);
-                                },
-                            },
-                            ...(noTree
-                                ? []
-                                : [
-                                    {
-                                        label: 'Make tree width fit to tree area',
-                                        type: 'checkbox',
-                                        checked: treeWidthMatchesArea,
-                                        onClick: () => {
-                                            model.setTreeWidthMatchesArea(!treeWidthMatchesArea);
-                                        },
-                                    },
-                                ]),
-                        ],
-                    },
-                    {
-                        label: 'MSA settings',
-                        type: 'subMenu',
-                        icon: GridOn,
-                        subMenu: [],
-                    },
-                    {
-                        label: 'More',
-                        icon: Settings,
-                        type: 'subMenu',
-                        subMenu: [
-                            {
-                                label: 'More settings',
-                                onClick: () => {
-                                    model.queueDialog(onClose => [
-                                        SettingsDialog,
-                                        {
-                                            model,
-                                            onClose,
-                                        },
-                                    ]);
-                                },
-                            },
-                        ],
-                    },
-                ],
-            },
             {
                 label: 'Metadata',
                 icon: Assignment,
@@ -136,7 +42,19 @@ const HeaderMenu = observer(({ model }) => {
                 },
             },
             {
-                label: ' tracks',
+                label: 'More settings',
+                onClick: () => {
+                    model.queueDialog(onClose => [
+                        SettingsDialog,
+                        {
+                            model,
+                            onClose,
+                        },
+                    ]);
+                },
+            },
+            {
+                label: 'Extra tracks',
                 icon: List,
                 onClick: () => {
                     model.queueDialog(onClose => [

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

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

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

package/dist/components/header/MSAMenu.js

@@ -0,0 +1,44 @@
+import React from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import { observer } from 'mobx-react';
+import { GridOn } from '@mui/icons-material';
+const MSAMenu = observer(function ({ model }) {
+    const { drawMsaLetters, contrastLettering, hideGaps, bgColor } = model;
+    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, menuItems: [
+            {
+                label: 'Draw letters',
+                type: 'checkbox',
+                checked: drawMsaLetters,
+                onClick: () => {
+                    model.setDrawMsaLetters(!drawMsaLetters);
+                },
+            },
+            {
+                label: 'Color letters instead of background of tiles',
+                type: 'checkbox',
+                checked: !bgColor,
+                onClick: () => {
+                    model.setBgColor(!bgColor);
+                },
+            },
+            {
+                label: 'Use contrast lettering',
+                type: 'checkbox',
+                checked: contrastLettering,
+                onClick: () => {
+                    model.setContrastLettering(!contrastLettering);
+                },
+            },
+            {
+                label: 'Enable hiding gappy columns?',
+                type: 'checkbox',
+                checked: hideGaps,
+                onClick: () => {
+                    model.setHideGaps(!hideGaps);
+                },
+            },
+        ] },
+        React.createElement(GridOn, null)));
+});
+export default MSAMenu;
+//# sourceMappingURL=MSAMenu.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"MSAMenu.js","sourceRoot":"","sources":["../../../src/components/header/MSAMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAA;AAI5C,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,cAAc,EAAE,iBAAiB,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACtE,OAAO,CACL,oBAAC,mBAAmB,IAClB,mBAAmB,EAAE,KAAK,EAC1B,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,cAAc;gBACrB,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,cAAc;gBACvB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;gBAC1C,CAAC;aACF;YACD;gBACE,KAAK,EAAE,8CAA8C;gBACrD,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,CAAC,OAAO;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,UAAU,CAAC,CAAC,OAAO,CAAC,CAAA;gBAC5B,CAAC;aACF;YACD;gBACE,KAAK,EAAE,wBAAwB;gBAC/B,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,iBAAiB;gBAC1B,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,oBAAoB,CAAC,CAAC,iBAAiB,CAAC,CAAA;gBAChD,CAAC;aACF;YACD;gBACE,KAAK,EAAE,8BAA8B;gBACrC,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,QAAQ;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;gBAC9B,CAAC;aACF;SACF;QAED,oBAAC,MAAM,OAAG,CACU,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

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

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

package/dist/components/header/TreeMenu.js

@@ -0,0 +1,64 @@
+import React from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import AccountTree from '@mui/icons-material/AccountTree';
+import { observer } from 'mobx-react';
+const TreeMenu = observer(({ model }) => {
+    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, treeWidthMatchesArea, noTree, } = model;
+    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, menuItems: [
+            {
+                label: 'Show branch length',
+                type: 'checkbox',
+                checked: showBranchLen,
+                onClick: () => {
+                    model.setShowBranchLen(!showBranchLen);
+                },
+            },
+            {
+                label: 'Show tree',
+                type: 'checkbox',
+                checked: drawTree,
+                onClick: () => {
+                    model.setDrawTree(!drawTree);
+                },
+            },
+            {
+                label: 'Draw clickable bubbles on tree branches',
+                type: 'checkbox',
+                checked: drawNodeBubbles,
+                onClick: () => {
+                    model.setDrawNodeBubbles(!drawNodeBubbles);
+                },
+            },
+            {
+                label: 'Tree labels align right',
+                type: 'checkbox',
+                checked: labelsAlignRight,
+                onClick: () => {
+                    model.setLabelsAlignRight(!labelsAlignRight);
+                },
+            },
+            {
+                label: 'Draw labels',
+                type: 'checkbox',
+                checked: drawLabels,
+                onClick: () => {
+                    model.setDrawLabels(!drawLabels);
+                },
+            },
+            ...(noTree
+                ? []
+                : [
+                    {
+                        label: 'Make tree width fit to tree area',
+                        type: 'checkbox',
+                        checked: treeWidthMatchesArea,
+                        onClick: () => {
+                            model.setTreeWidthMatchesArea(!treeWidthMatchesArea);
+                        },
+                    },
+                ]),
+        ] },
+        React.createElement(AccountTree, null)));
+});
+export default TreeMenu;
+//# sourceMappingURL=TreeMenu.js.map

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

@@ -0,0 +1 @@
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package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -18,13 +18,14 @@ export function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, high
 }
 function drawTiles({ model, ctx, visibleLeaves, }) {
     const { subFeatureRows, colWidth, rowHeight, fillPalette, strokePalette, tidyFilteredGatheredInterProAnnotations, } = model;
-    for (const node of visibleLeaves) {
+    for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
+        const node = visibleLeaves[i];
         const { x, data: { name }, } = node;
         const y = x;
         const entry = tidyFilteredGatheredInterProAnnotations[name];
-        let j = 0;
         if (entry) {
-            for (const { start, end, accession } of entry) {
+            for (let j = 0, l2 = entry.length; j < l2; j++) {
+                const { start, end, accession } = entry[j];
                 const m1 = model.seqCoordToRowSpecificGlobalCoord(name, start - 1);
                 const m2 = model.seqCoordToRowSpecificGlobalCoord(name, end);
                 const x = m1 * colWidth;
@@ -35,7 +36,6 @@ function drawTiles({ model, ctx, visibleLeaves, }) {
                 const lw = colWidth * (m2 - m1);
                 ctx.fillRect(x, t, lw, h);
                 ctx.strokeRect(x, t, lw, h);
-                j++;
             }
         }
     }

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

@@ -1 +1 @@
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+{"version":3,"file":"renderBoxFeatureCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderBoxFeatureCanvasBlock.ts"],"names":[],"mappings":"AAIA,MAAM,UAAU,2BAA2B,CAAC,EAC1C,KAAK,EACL,OAAO,EACP,OAAO,EACP,GAAG,EACH,0BAA0B,EAC1B,kBAAkB,GAQnB;IACC,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,kBAAkB,EAAE,WAAW,EAAE,GACrE,KAAK,CAAA;IACP,IAAI,WAAW,EAAE,CAAC;QAChB,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;QAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;QAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;QAEhD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;QACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;QAC3E,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAEhD,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,GAAG,EACH,aAAa,GAKd;IACC,MAAM,EACJ,cAAc,EACd,QAAQ,EACR,SAAS,EACT,WAAW,EACX,aAAa,EACb,uCAAuC,GACxC,GAAG,KAAK,CAAA;IAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EACJ,CAAC,EACD,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,CAAE,CAAA;QAEZ,MAAM,KAAK,GAAG,uCAAuC,CAAC,IAAI,CAAC,CAAA;QAE3D,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC/C,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;gBAC3C,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,IAAI,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;gBAClE,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;gBAC5D,MAAM,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAA;gBACvB,GAAG,CAAC,SAAS,GAAG,WAAW,CAAC,SAAS,CAAE,CAAA;gBACvC,GAAG,CAAC,WAAW,GAAG,aAAa,CAAC,SAAS,CAAE,CAAA;gBAC3C,MAAM,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;gBACxC,MAAM,CAAC,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtD,MAAM,EAAE,GAAG,QAAQ,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;gBAC/B,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;gBACzB,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;YAC7B,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/components/msa/renderMSABlock.js

@@ -1,6 +1,6 @@
 import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
 export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, leaves, } = model;
+    const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, leaves, bgColor, } = model;
     const k = highResScaleFactorOverride || highResScaleFactor;
     const bx = blockSizeXOverride || blockSize;
     const by = blockSizeYOverride || blockSize;
@@ -8,7 +8,7 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     ctx.scale(k, k);
     ctx.translate(-offsetX, rowHeight / 2 - offsetY);
     ctx.textAlign = 'center';
-    ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
+    ctx.font = ctx.font.replace(/\d+px/, `${bgColor ? '' : 'bold '}${fontSize}px`);
     const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
     const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight));
     const xStart = Math.max(0, Math.floor(offsetX / colWidth));
@@ -40,25 +40,28 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
 }
 function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, }) {
     const { bgColor, colorSchemeName, colorScheme, columns, colWidth, rowHeight, } = model;
-    for (const node of visibleLeaves) {
+    for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
+        const node = visibleLeaves[i];
         const { data: { name }, } = node;
         const y = node.x;
         const str = columns[name]?.slice(xStart, xEnd);
         if (str) {
-            for (let i = 0; i < str.length; i++) {
+            for (let i = 0, l2 = str.length; i < l2; i++) {
                 const letter = str[i];
-                const color = colorSchemeName === 'clustalx_protein_dynamic'
+                const r1 = colorSchemeName === 'clustalx_protein_dynamic';
+                const r2 = colorSchemeName === 'percent_identity_dynamic';
+                const color = r1
                     ? getClustalXColor(
                     // use model.colStats dot notation here: delay use of colStats
                     // until absolutely needed
                     model.colStats[xStart + i], model.colStatsSums[xStart + i], model, name, xStart + i)
-                    : colorSchemeName === 'percent_identity_dynamic'
+                    : r2
                         ? getPercentIdentityColor(
                         // use model.colStats dot notation here: delay use of
                         // colStats until absolutely needed
                         model.colStats[xStart + i], model.colStatsSums[xStart + i], model, name, xStart + i)
                         : colorScheme[letter.toUpperCase()];
-                if (bgColor) {
+                if (bgColor || r1 || r2) {
                     ctx.fillStyle = color || theme.palette.background.default;
                     ctx.fillRect(i * colWidth + offsetX - (offsetX % colWidth), y - rowHeight, colWidth, rowHeight);
                 }
@@ -69,12 +72,13 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
 function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart, xEnd, }) {
     const { bgColor, actuallyShowDomains, showMsaLetters, colorScheme, columns, colWidth, contrastLettering, rowHeight, } = model;
     if (showMsaLetters) {
-        for (const node of visibleLeaves) {
+        for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
+            const node = visibleLeaves[i];
             const { data: { name }, } = node;
             const y = node.x;
             const str = columns[name]?.slice(xStart, xEnd);
             if (str) {
-                for (let i = 0; i < str.length; i++) {
+                for (let i = 0, l2 = str.length; i < l2; i++) {
                     const letter = str[i];
                     const color = colorScheme[letter.toUpperCase()];
                     const contrast = contrastLettering