react-msaview 4.4.0 → 4.4.1

package/dist/rowCoordinateCalculations.test.js.map

@@ -1 +1 @@
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package/dist/seqCoordToRowSpecificGlobalCoord.d.ts

@@ -0,0 +1,4 @@
+export declare function seqCoordToRowSpecificGlobalCoord({ row, position, }: {
+    row: string;
+    position: number;
+}): number;

package/dist/seqCoordToRowSpecificGlobalCoord.js

@@ -0,0 +1,15 @@
+import { isBlank } from './util';
+export function seqCoordToRowSpecificGlobalCoord({ row, position, }) {
+    let k = 0;
+    let i = 0;
+    for (; k < position; i++) {
+        if (!isBlank(row[i])) {
+            k++;
+        }
+        else if (k >= position) {
+            break;
+        }
+    }
+    return i;
+}
+//# sourceMappingURL=seqCoordToRowSpecificGlobalCoord.js.map

package/dist/seqCoordToRowSpecificGlobalCoord.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seqCoordToRowSpecificGlobalCoord.js","sourceRoot":"","sources":["../src/seqCoordToRowSpecificGlobalCoord.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA;AAEhC,MAAM,UAAU,gCAAgC,CAAC,EAC/C,GAAG,EACH,QAAQ,GAIT;IACC,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,OAAO,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;QACzB,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,CAAC,IAAI,QAAQ,EAAE,CAAC;YACzB,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}

package/dist/seqCoordToRowSpecificGlobalCoord.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/seqCoordToRowSpecificGlobalCoord.test.js

@@ -0,0 +1,42 @@
+import { describe, expect, test } from 'vitest';
+import { seqCoordToRowSpecificGlobalCoord } from './seqCoordToRowSpecificGlobalCoord';
+describe('seqCoordToRowSpecificGlobalCoord', () => {
+    test('converts sequence coordinate to global coordinate with no gaps', () => {
+        const row = 'ATGCATGC';
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(3);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 8 })).toBe(8);
+    });
+    test('converts sequence coordinate to global coordinate with gaps', () => {
+        const row = 'A-TG-CA-TGC';
+        // A(0) -(1) T(2) G(3) -(4) C(5) A(6) -(7) T(8) G(9) C(10)
+        // Sequence positions: A(0) T(1) G(2) C(3) A(4) T(5) G(6) C(7)
+        // Position 0 (first A) -> Global index 0
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
+        // Position 1 (T after first gap) -> Global index 2
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(1);
+        // Position 3 (C after second gap) -> Global index 5
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(4);
+        // Position 5 (T after third gap) -> Global index 8
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 5 })).toBe(7);
+        // Position 8 (end of sequence) -> Global index 11
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 8 })).toBe(11);
+    });
+    test('handles empty row', () => {
+        expect(seqCoordToRowSpecificGlobalCoord({ row: '', position: 0 })).toBe(0);
+    });
+    test('handles row with only gaps', () => {
+        const row = '---..--';
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
+    });
+    test('handles mixed gap characters', () => {
+        const row = 'A-.G-C.';
+        // A(0) -(1) .(2) G(3) -(4) C(5) .(6)
+        // Sequence positions: A(0) G(1) C(2)
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(1);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 2 })).toBe(4);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(6);
+    });
+});
+//# sourceMappingURL=seqCoordToRowSpecificGlobalCoord.test.js.map

package/dist/seqCoordToRowSpecificGlobalCoord.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seqCoordToRowSpecificGlobalCoord.test.js","sourceRoot":"","sources":["../src/seqCoordToRowSpecificGlobalCoord.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,gCAAgC,EAAE,MAAM,oCAAoC,CAAA;AAErF,QAAQ,CAAC,kCAAkC,EAAE,GAAG,EAAE;IAChD,IAAI,CAAC,gEAAgE,EAAE,GAAG,EAAE;QAC1E,MAAM,GAAG,GAAG,UAAU,CAAA;QACtB,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACxE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6DAA6D,EAAE,GAAG,EAAE;QACvE,MAAM,GAAG,GAAG,aAAa,CAAA;QACzB,0DAA0D;QAC1D,8DAA8D;QAE9D,yCAAyC;QACzC,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAEtE,mDAAmD;QACnD,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAEtE,oDAAoD;QACpD,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAEtE,mDAAmD;QACnD,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAEtE,kDAAkD;QAClD,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACzE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC5E,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,GAAG,GAAG,SAAS,CAAA;QACrB,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACxE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACxC,MAAM,GAAG,GAAG,SAAS,CAAA;QACrB,qCAAqC;QACrC,qCAAqC;QAErC,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACxE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}

package/dist/util.d.ts

@@ -12,13 +12,8 @@ export declare function skipBlanks(blanks: number[], arg: string | string[]): st
 export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;
 export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
 export declare function collapse(d: HierarchyNode<NodeWithIds>): void;
-export declare function clamp(min: number, num: number, max: number): number;
 export declare function len(a: {
     end: number;
     start: number;
 }): number;
-export declare function localStorageGetItem(item: string): string | null | undefined;
-export declare function localStorageGetBoolean(key: string, defaultVal: boolean): boolean;
-export declare function localStorageSetItem(str: string, item: string): void;
-export declare function localStorageSetBoolean(key: string, value: boolean): void;
-export declare function isGzip(buf: Uint8Array): boolean;
+export declare function isBlank(s?: string): s is "-" | ".";

package/dist/util.js

@@ -23,7 +23,7 @@ export function colorContrast(colorScheme, theme) {
 export function skipBlanks(blanks, arg) {
     let s = '';
     let b = 0;
-    for (let j = 0; j < arg.length; j++) {
+    for (let j = 0, l = arg.length; j < l; j++) {
         if (j === blanks[b]) {
             b++;
         }
@@ -57,29 +57,12 @@ export function collapse(d) {
         d.children = null;
     }
 }
-export function clamp(min, num, max) {
-    return Math.min(Math.max(num, min), max);
-}
 export function len(a) {
     return a.end - a.start;
 }
-export function localStorageGetItem(item) {
-    return typeof localStorage !== 'undefined'
-        ? localStorage.getItem(item)
-        : undefined;
-}
-export function localStorageGetBoolean(key, defaultVal) {
-    return Boolean(JSON.parse(localStorageGetItem(key) || JSON.stringify(defaultVal)));
-}
-export function localStorageSetItem(str, item) {
-    if (typeof localStorage !== 'undefined') {
-        localStorage.setItem(str, item);
-    }
-}
-export function localStorageSetBoolean(key, value) {
-    localStorageSetItem(key, JSON.stringify(value));
-}
-export function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+// https://sonnhammer.sbc.su.se/Stockholm.html
+// gaps can be a . or - in stockholm
+export function isBlank(s) {
+    return s === '-' || s === '.';
 }
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAM9B,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,MAAM,UAAU,SAAS,CACvB,GAAsB,EACtB,EAAsC;IAEtC,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,EAAE,GAAG,GAAG,MAAM,IAAI,KAAK,EAAE,CAAA;IAE/B,OAAO;QACL,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,QAAQ,EACN,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC1B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,IAAI,EAAE;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,WAAmC,EACnC,KAAY;IAEZ,OAAO,SAAS,CAAC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QACjD,MAAM;QACN,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;KACrD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,MAAgB,EAAE,GAAsB;IACjE,IAAI,CAAC,GAAG,EAAE,CAAA;IACV,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,IAAI,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AAED,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,CAA6B;IACpD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,mBAAmB;QACnB,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,QAAQ,CAAA;QACxB,mBAAmB;QACnB,CAAC,CAAC,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC;AAED,8CAA8C;AAC9C,oCAAoC;AACpC,MAAM,UAAU,OAAO,CAAC,CAAU;IAChC,OAAO,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAA;AAC/B,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.4.0";
+export declare const version = "4.4.1";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '4.4.0';
+export const version = '4.4.1';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "4.4.0",
+  "version": "4.4.1",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",

package/src/colorSchemes.ts

@@ -2,7 +2,7 @@ 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])
 
@@ -518,7 +518,7 @@ export function getPercentIdentityColor(
   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/src/components/VerticalScrollbar.tsx

@@ -1,9 +1,8 @@
 import React, { useEffect, useRef, useState } from 'react'
 
+import { clamp } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
-import { clamp } from '../util'
-
 import type { MsaViewModel } from '../model'
 
 const VerticalScrollbar = observer(({ model }: { model: MsaViewModel }) => {
@@ -28,8 +27,8 @@ const VerticalScrollbar = observer(({ model }: { model: MsaViewModel }) => {
           window.requestAnimationFrame(() => {
             model.setScrollY(
               clamp(
-                -totalHeight,
                 mouseDown.scrollY - (event.clientY - mouseDown.clientY) / unit,
+                -totalHeight,
                 0,
               ),
             )

package/src/components/header/ColorMenu.tsx

@@ -0,0 +1,33 @@
+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'
+
+import type { MsaViewModel } from '../../model'
+
+const ColorMenu = observer(({ model }: { model: MsaViewModel }) => {
+  const { colorSchemeName } = model
+  return (
+    <CascadingMenuButton
+      closeAfterItemClick={false}
+      menuItems={Object.keys(colorSchemes).map(
+        option =>
+          ({
+            label: option,
+            type: 'radio',
+            checked: colorSchemeName === option,
+            onClick: () => {
+              model.setColorSchemeName(option)
+            },
+          }) as const,
+      )}
+    >
+      <Palette />
+    </CascadingMenuButton>
+  )
+})
+
+export default ColorMenu

package/src/components/header/Header.tsx

@@ -5,11 +5,13 @@ 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'
@@ -26,7 +28,9 @@ const Header = observer(function ({ model }: { model: MsaViewModel }) {
   return (
     <div ref={ref} style={{ display: 'flex' }}>
       <HeaderMenu model={model} />
-      <SettingsMenu model={model} />
+      <ColorMenu model={model} />
+      <TreeMenu model={model} />
+      <MSAMenu model={model} />
       <ZoomControls model={model} />
       {model.showZoomStar ? <ZoomStar model={model} /> : null}
       <ZoomMenu model={model} />

package/src/components/header/HeaderInfoArea.tsx

@@ -19,8 +19,11 @@ const HeaderInfoArea = observer(function ({ model }: { model: MsaViewModel }) {
   return mouseOverRowName && mouseCol !== undefined ? (
     <Typography className={classes.margin}>
       {mouseOverRowName}:
-      {model.mouseOverCoordToGapRemovedRowCoord(mouseOverRowName, mouseCol)} (
-      {model.mouseOverCoordToRowLetter(mouseOverRowName, mouseCol)})
+      {model.mouseOverCoordToGapRemovedRowCoordOneBased(
+        mouseOverRowName,
+        mouseCol,
+      )}{' '}
+      ({model.mouseOverCoordToRowLetter(mouseOverRowName, mouseCol)})
     </Typography>
   ) : null
 })

package/src/components/header/HeaderMenu.tsx

@@ -1,16 +1,13 @@
 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'
@@ -18,30 +15,18 @@ import { observer } from 'mobx-react'
 import type { MsaViewModel } from '../../model'
 
 // 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 }: { model: MsaViewModel }) => {
-  const {
-    drawTree,
-    showBranchLen,
-    labelsAlignRight,
-    drawNodeBubbles,
-    showDomains,
-    actuallyShowDomains,
-    subFeatureRows,
-    drawLabels,
-    treeWidthMatchesArea,
-    noDomains,
-    noTree,
-  } = model
+  const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model
   return (
     <CascadingMenuButton
       menuItems={[
@@ -52,98 +37,6 @@ const HeaderMenu = observer(({ model }: { model: MsaViewModel }) => {
             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' as const,
-                        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,
@@ -158,7 +51,19 @@ const HeaderMenu = observer(({ model }: { model: MsaViewModel }) => {
           },
         },
         {
-          label: ' tracks',
+          label: 'More settings',
+          onClick: () => {
+            model.queueDialog(onClose => [
+              SettingsDialog,
+              {
+                model,
+                onClose,
+              },
+            ])
+          },
+        },
+        {
+          label: 'Extra tracks',
           icon: List,
           onClick: () => {
             model.queueDialog(onClose => [

package/src/components/header/MSAMenu.tsx

@@ -0,0 +1,55 @@
+import React from 'react'
+
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'
+import { observer } from 'mobx-react'
+
+import { GridOn } from '@mui/icons-material'
+
+import type { MsaViewModel } from '../../model'
+
+const MSAMenu = observer(function ({ model }: { model: MsaViewModel }) {
+  const { drawMsaLetters, contrastLettering, hideGaps, bgColor } = model
+  return (
+    <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)
+          },
+        },
+      ]}
+    >
+      <GridOn />
+    </CascadingMenuButton>
+  )
+})
+
+export default MSAMenu

package/src/components/header/TreeMenu.tsx

@@ -0,0 +1,82 @@
+import React from 'react'
+
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'
+import AccountTree from '@mui/icons-material/AccountTree'
+import { observer } from 'mobx-react'
+
+import type { MsaViewModel } from '../../model'
+
+const TreeMenu = observer(({ model }: { model: MsaViewModel }) => {
+  const {
+    drawTree,
+    showBranchLen,
+    labelsAlignRight,
+    drawNodeBubbles,
+    drawLabels,
+    treeWidthMatchesArea,
+    noTree,
+  } = model
+  return (
+    <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' as const,
+                checked: treeWidthMatchesArea,
+                onClick: () => {
+                  model.setTreeWidthMatchesArea(!treeWidthMatchesArea)
+                },
+              },
+            ]),
+      ]}
+    >
+      <AccountTree />
+    </CascadingMenuButton>
+  )
+})
+
+export default TreeMenu

package/src/components/msa/renderBoxFeatureCanvasBlock.ts

@@ -56,7 +56,8 @@ function drawTiles({
     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 },
@@ -65,9 +66,9 @@ function drawTiles({
 
     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
@@ -78,7 +79,6 @@ function drawTiles({
         const lw = colWidth * (m2 - m1)
         ctx.fillRect(x, t, lw, h)
         ctx.strokeRect(x, t, lw, h)
-        j++
       }
     }
   }