react-msaview 5.0.16 → 5.1.1

package/dist/clustalX.d.ts

@@ -0,0 +1,5 @@
+/**
+ * Computes the ClustalX letter->color map for a single alignment column given
+ * its residue counts (`stats`) and total residue count (`total`).
+ */
+export declare function clustalXColumnColors(stats: Record<string, number>, total: number): Record<string, string>;

package/dist/clustalX.js

@@ -0,0 +1,88 @@
+// ClustalX consensus coloring.
+// ref http://www.jalview.org/help/html/colourSchemes/clustal.html
+const BLUE = 'rgb(128,179,230)';
+const RED = '#d88';
+const MAGENTA_E = 'rgb(192, 72, 192)';
+const MAGENTA_D = 'rgb(204, 77, 204)';
+const GREEN = '#8f8';
+const GREEN_ST = 'rgb(26,204,26)';
+const PINK = 'rgb(240, 128, 128)';
+const ORANGE = 'rgb(240, 144, 72)';
+const YELLOW = 'rgb(204, 204, 0)';
+const CYAN = 'rgb(26, 179, 179)';
+/**
+ * Computes the ClustalX letter->color map for a single alignment column given
+ * its residue counts (`stats`) and total residue count (`total`).
+ */
+export function clustalXColumnColors(stats, total) {
+    const { W = 0, L = 0, V = 0, I = 0, M = 0, A = 0, F = 0, C = 0, H = 0, P = 0, R = 0, K = 0, Q = 0, E = 0, D = 0, T = 0, S = 0, G = 0, Y = 0, N = 0, } = stats;
+    const hydrophobic = W + L + V + I + M + A + F + C + H + P + Y;
+    const KR = K + R;
+    const QE = Q + E;
+    const ED = E + D;
+    const TS = T + S;
+    const p = (n) => n / total;
+    const colors = {};
+    if (p(hydrophobic) > 0.6) {
+        colors.W = BLUE;
+        colors.L = BLUE;
+        colors.V = BLUE;
+        colors.A = BLUE;
+        colors.I = BLUE;
+        colors.M = BLUE;
+        colors.F = BLUE;
+        colors.C = BLUE;
+    }
+    if (p(KR) > 0.6 || p(K) > 0.8 || p(R) > 0.8 || p(Q) > 0.8) {
+        colors.K = RED;
+        colors.R = RED;
+    }
+    if (p(KR) > 0.6 || p(QE) > 0.5 || p(E) > 0.8 || p(Q) > 0.8 || p(D) > 0.8) {
+        colors.E = MAGENTA_E;
+    }
+    if (p(KR) > 0.6 || p(ED) > 0.5 || p(K) > 0.8 || p(R) > 0.8 || p(Q) > 0.8) {
+        colors.D = MAGENTA_D;
+    }
+    if (p(N) > 0.5 || p(Y) > 0.85) {
+        colors.N = GREEN;
+    }
+    if (p(KR) > 0.6 ||
+        p(QE) > 0.6 ||
+        p(Q) > 0.85 ||
+        p(E) > 0.85 ||
+        p(K) > 0.85 ||
+        p(R) > 0.85) {
+        colors.Q = GREEN;
+    }
+    if (p(hydrophobic) > 0.6 || p(TS) > 0.5 || p(S) > 0.85 || p(T) > 0.85) {
+        colors.S = GREEN_ST;
+        colors.T = GREEN_ST;
+    }
+    if (p(C) > 0.85) {
+        colors.C = PINK;
+    }
+    if (G > 0) {
+        colors.G = ORANGE;
+    }
+    if (P > 0) {
+        colors.P = YELLOW;
+    }
+    if (p(hydrophobic) > 0.6 ||
+        p(W) > 0.85 ||
+        p(Y) > 0.85 ||
+        p(A) > 0.85 ||
+        p(C) > 0.85 ||
+        p(P) > 0.85 ||
+        p(Q) > 0.85 ||
+        p(F) > 0.85 ||
+        p(H) > 0.85 ||
+        p(I) > 0.85 ||
+        p(L) > 0.85 ||
+        p(M) > 0.85 ||
+        p(V) > 0.85) {
+        colors.H = CYAN;
+        colors.Y = CYAN;
+    }
+    return colors;
+}
+//# sourceMappingURL=clustalX.js.map

package/dist/clustalX.js.map

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

@@ -22,8 +22,8 @@ export default function SequenceTextArea({ str }) {
     const removeGaps = (s) => s.replaceAll('-', '').replaceAll('.', '');
     const disp = str
         .map(([s1, s2]) => [s1, showGaps ? s2 : removeGaps(s2)])
-        .filter(f => (showEmpty ? true : !!f[1]))
-        .map(([s1, s2]) => `>${s1}\n${showGaps ? s2 : removeGaps(s2)}`)
+        .filter(([, s2]) => showEmpty || !!s2)
+        .map(([s1, s2]) => `>${s1}\n${s2}`)
         .join('\n');
     return (React.createElement(React.Fragment, null,
         React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {

package/dist/components/SequenceTextArea.js.map

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

@@ -1,15 +1,13 @@
-import React, { useEffect, useMemo, useRef } from 'react';
-import { useTheme } from '@mui/material';
+import React, { useEffect, useRef } from 'react';
 import { observer } from 'mobx-react';
-import { colorContrast } from "../util.js";
+import { useColorContrast } from "../useColorContrast.js";
 import { drawTextTrackContent } from "./tracks/renderTracksSvg.js";
 const AnnotationBlock = observer(function ({ track, model, offsetX, }) {
     const { blockSize, scrollX, bgColor, colorScheme: modelColorScheme, colWidth, fontSize, rowHeight, highResScaleFactor, } = model;
     const { model: { customColorScheme, data }, } = track;
     const colorScheme = customColorScheme || modelColorScheme;
-    const theme = useTheme();
     const ref = useRef(null);
-    const contrastScheme = useMemo(() => colorContrast(colorScheme, theme), [colorScheme, theme]);
+    const { contrastScheme } = useColorContrast(colorScheme);
     useEffect(() => {
         if (!ref.current) {
             return;

package/dist/components/TextTrack.js.map

@@ -1 +1 @@
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package/dist/components/Track.d.ts

@@ -1,7 +1,8 @@
 import React from 'react';
 import type { MsaViewModel } from '../model.ts';
+import type { BasicTrack } from '../types.ts';
 declare const Track: ({ model, track, }: {
     model: MsaViewModel;
-    track: any;
+    track: BasicTrack;
 }) => React.JSX.Element;
 export default Track;

package/dist/components/Track.js

@@ -49,13 +49,13 @@ const TrackLabel = observer(function TrackLabel({ model, track, }) {
 });
 const Track = observer(function ({ model, track, }) {
     const { resizeHandleWidth, colWidth, scrollX, numColumns } = model;
-    const { model: { height, error }, } = track;
+    const { model: { height }, } = track;
     const ref = useRef(null);
     const onScrollX = useCallback((d) => {
         model.doScrollX(d);
     }, [model]);
     useWheelScroll({ ref, onScrollX });
-    return (React.createElement("div", { key: track.id, style: { display: 'flex', height } },
+    return (React.createElement("div", { style: { display: 'flex', height } },
         React.createElement(TrackLabel, { model: model, track: track }),
         React.createElement("div", { style: { width: resizeHandleWidth, flexShrink: 0 } }),
         React.createElement("div", { ref: ref, onMouseMove: event => {
@@ -73,7 +73,8 @@ const Track = observer(function ({ model, track, }) {
                 }
             }, onMouseLeave: () => {
                 model.setMousePos(undefined, undefined);
-            } }, error ? (React.createElement("div", { style: { color: 'red', fontSize: 10 } }, `${error}`)) : (React.createElement(track.ReactComponent, { model: model, track: track })))));
+            } },
+            React.createElement(track.ReactComponent, { model: model, track: track }))));
 });
 export default Track;
 //# sourceMappingURL=Track.js.map

package/dist/components/Track.js.map

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package/dist/components/VerticalScrollbar.js

@@ -1,41 +1,19 @@
-import React, { useEffect, useRef, useState } from 'react';
+import React, { useCallback, useState } from 'react';
 import { clamp } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
+import { useDragScroll } from "../useDragScroll.js";
 const VerticalScrollbar = observer(({ model }) => {
     const { msaAreaHeight, scrollY, totalHeight } = model;
     const [hovered, setHovered] = useState(false);
-    const scheduled = useRef(false);
-    const [mouseDown, setMouseDown] = useState();
     const fill = 'rgba(66, 119, 127, 0.3)';
     const unit = msaAreaHeight / totalHeight;
     const top = -scrollY;
     const bottom = top + msaAreaHeight;
     const t = top * unit;
     const b = bottom * unit;
-    useEffect(() => {
-        function fn(event) {
-            if (mouseDown !== undefined) {
-                if (!scheduled.current) {
-                    scheduled.current = true;
-                    window.requestAnimationFrame(() => {
-                        model.setScrollY(clamp(mouseDown.scrollY - (event.clientY - mouseDown.clientY) / unit, -totalHeight, 0));
-                        scheduled.current = false;
-                    });
-                }
-            }
-        }
-        function fn2() {
-            setMouseDown(undefined);
-        }
-        if (mouseDown !== undefined) {
-            document.addEventListener('mousemove', fn);
-            document.addEventListener('mouseup', fn2);
-            return () => {
-                document.removeEventListener('mousemove', fn);
-                document.removeEventListener('mousemove', fn2);
-            };
-        }
-    }, [model, unit, totalHeight, mouseDown]);
+    const { startDrag } = useDragScroll('y', useCallback((delta, startScroll) => {
+        model.setScrollY(clamp(startScroll - delta / unit, -totalHeight, 0));
+    }, [model, unit, totalHeight]));
     return (React.createElement("div", { style: {
             position: 'relative',
             width: 20,
@@ -59,10 +37,7 @@ const VerticalScrollbar = observer(({ model }) => {
             }, onMouseOut: () => {
                 setHovered(false);
             }, onMouseDown: event => {
-                setMouseDown({
-                    clientY: event.clientY,
-                    scrollY: model.scrollY,
-                });
+                startDrag(event, model.scrollY);
             } })));
 });
 export default VerticalScrollbar;

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,WAAW,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEpD,OAAO,EAAE,KAAK,EAAE,MAAM,oBAAoB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAA;AAInD,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,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,MAAM,EAAE,SAAS,EAAE,GAAG,aAAa,CACjC,GAAG,EACH,WAAW,CACT,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,UAAU,CAAC,KAAK,CAAC,WAAW,GAAG,KAAK,GAAG,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,CAAA;IACtE,CAAC,EACD,CAAC,KAAK,EAAE,IAAI,EAAE,WAAW,CAAC,CAC3B,CACF,CAAA;IACD,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,SAAS,CAAC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAA;YACjC,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,iBAAiB,CAAA"}

package/dist/components/dialogs/InterProScanDialog.js

@@ -169,8 +169,7 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
                     handleClose();
                 } }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
+                    const controller = new AbortController();
                     (async () => {
                         try {
                             const { rows } = model;
@@ -186,9 +185,12 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
                                     .map(row => `>${row[0]}\n${row[1]}`)
                                     .join('\n'),
                                 onProgress: arg => {
-                                    model.setStatus(arg);
+                                    model.setStatus(arg
+                                        ? { ...arg, onCancel: () => { controller.abort(); } }
+                                        : undefined);
                                 },
                                 model,
+                                signal: controller.signal,
                             });
                         }
                         catch (e) {

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

@@ -1 +1 @@
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package/dist/components/header/HeaderStatusArea.js

@@ -1,6 +1,6 @@
 import React from 'react';
 import { LoadingEllipses } from '@jbrowse/core/ui';
-import { Typography } from '@mui/material';
+import { Button, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
@@ -15,7 +15,9 @@ const HeaderStatusArea = observer(({ model }) => {
     return status ? (React.createElement(Typography, { className: classes.margin },
         React.createElement(LoadingEllipses, { message: status.msg, component: "span" }),
         ' ',
-        status.url ? (React.createElement("a", { href: status.url, target: "_blank", rel: "noreferrer" }, "(status)")) : null)) : null;
+        status.url ? (React.createElement("a", { href: status.url, target: "_blank", rel: "noreferrer" }, "(status)")) : null,
+        ' ',
+        status.onCancel ? (React.createElement(Button, { size: "small", onClick: () => status.onCancel?.() }, "Cancel")) : null)) : null;
 });
 export default HeaderStatusArea;
 //# sourceMappingURL=HeaderStatusArea.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"HeaderStatusArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderStatusArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,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,gBAAgB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACvE,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QACnC,oBAAC,eAAe,IAAC,OAAO,EAAE,MAAM,CAAC,GAAG,EAAE,SAAS,EAAC,MAAM,GAAG;QAAC,GAAG;QAC5D,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CACZ,2BAAG,IAAI,EAAE,MAAM,CAAC,GAAG,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY,eAEjD,CACL,CAAC,CAAC,CAAC,IAAI,CACG,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}
+{"version":3,"file":"HeaderStatusArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderStatusArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,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,gBAAgB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACvE,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QACnC,oBAAC,eAAe,IAAC,OAAO,EAAE,MAAM,CAAC,GAAG,EAAE,SAAS,EAAC,MAAM,GAAG;QAAC,GAAG;QAC5D,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CACZ,2BAAG,IAAI,EAAE,MAAM,CAAC,GAAG,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY,eAEjD,CACL,CAAC,CAAC,CAAC,IAAI;QAAE,GAAG;QACZ,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CACjB,oBAAC,MAAM,IAAC,IAAI,EAAC,OAAO,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,aAE9C,CACV,CAAC,CAAC,CAAC,IAAI,CACG,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/header/MSASettingsMenu.js

@@ -2,34 +2,9 @@ import React from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 import Tune from '@mui/icons-material/Tune';
 import { observer } from 'mobx-react';
+import { msaSettingsMenuItems } from "./settingsMenuItems.js";
 const MSASettingsMenu = observer(function ({ model }) {
-    const { drawMsaLetters, hideGaps, bgColor } = model;
-    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, 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: 'Enable hiding gappy columns?',
-                type: 'checkbox',
-                checked: hideGaps,
-                onClick: () => {
-                    model.setHideGaps(!hideGaps);
-                },
-            },
-        ] },
+    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: msaSettingsMenuItems(model) },
         React.createElement(Tune, null)));
 });
 export default MSASettingsMenu;

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

@@ -1 +1 @@
-{"version":3,"file":"MSASettingsMenu.js","sourceRoot":"","sources":["../../../src/components/header/MSASettingsMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC3E,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnD,OAAO,CACL,oBAAC,mBAAmB,IAClB,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;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,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,IAAI,OAAG,CACY,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}
+{"version":3,"file":"MSASettingsMenu.js","sourceRoot":"","sources":["../../../src/components/header/MSASettingsMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAA;AAI7D,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC3E,OAAO,CACL,oBAAC,mBAAmB,IAClB,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,oBAAoB,CAAC,KAAK,CAAC;QAEtC,oBAAC,IAAI,OAAG,CACY,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/header/SettingsMenu.js

@@ -4,9 +4,10 @@ import AccountTree from '@mui/icons-material/AccountTree';
 import Palette from '@mui/icons-material/Palette';
 import Settings from '@mui/icons-material/Settings';
 import { observer } from 'mobx-react';
+import { msaSettingsMenuItems, treeSettingsMenuItems, } from "./settingsMenuItems.js";
 import colorSchemes from "../../colorSchemes.js";
 const SettingsMenu = observer(function ({ model }) {
-    const { colorSchemeName, drawMsaLetters, hideGaps, bgColor, drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, } = model;
+    const { colorSchemeName } = model;
     return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, menuItems: [
             {
                 label: 'Color scheme',
@@ -24,79 +25,13 @@ const SettingsMenu = observer(function ({ model }) {
             {
                 label: 'MSA settings',
                 type: 'subMenu',
-                subMenu: [
-                    {
-                        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: 'Enable hiding gappy columns?',
-                        type: 'checkbox',
-                        checked: hideGaps,
-                        onClick: () => {
-                            model.setHideGaps(!hideGaps);
-                        },
-                    },
-                ],
+                subMenu: msaSettingsMenuItems(model),
             },
             {
                 label: 'Tree settings',
                 type: 'subMenu',
                 icon: AccountTree,
-                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);
-                        },
-                    },
-                ],
+                subMenu: treeSettingsMenuItems(model),
             },
         ] },
         React.createElement(Settings, null)));

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

@@ -1 +1 @@
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+{"version":3,"file":"SettingsMenu.js","sourceRoot":"","sources":["../../../src/components/header/SettingsMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,OAAO,MAAM,6BAA6B,CAAA;AACjD,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,oBAAoB,EACpB,qBAAqB,GACtB,MAAM,wBAAwB,CAAA;AAC/B,OAAO,YAAY,MAAM,uBAAuB,CAAA;AAIhD,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACxE,MAAM,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACjC,OAAO,CACL,oBAAC,mBAAmB,IAClB,mBAAmB,EAAE,KAAK,EAC1B,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,cAAc;gBACrB,IAAI,EAAE,OAAO;gBACb,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CACpC,MAAM,CAAC,EAAE,CACP,CAAC;oBACC,KAAK,EAAE,MAAM;oBACb,IAAI,EAAE,OAAO;oBACb,OAAO,EAAE,eAAe,KAAK,MAAM;oBACnC,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;oBAClC,CAAC;iBACF,CAAU,CACd;aACF;YACD;gBACE,KAAK,EAAE,cAAc;gBACrB,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE,oBAAoB,CAAC,KAAK,CAAC;aACrC;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,SAAS;gBACf,IAAI,EAAE,WAAW;gBACjB,OAAO,EAAE,qBAAqB,CAAC,KAAK,CAAC;aACtC;SACF;QAED,oBAAC,QAAQ,OAAG,CACQ,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/components/header/TreeSettingsMenu.js

@@ -2,49 +2,11 @@ import React from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 import AccountTree from '@mui/icons-material/AccountTree';
 import { observer } from 'mobx-react';
+import { treeSettingsMenuItems } from "./settingsMenuItems.js";
 const TreeSettingsMenu = observer(function ({ model, }) {
-    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, rows, } = model;
+    const { rows } = model;
     return (React.createElement(CascadingMenuButton, { closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, 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);
-                },
-            },
+            ...treeSettingsMenuItems(model),
             ...(rows.length >= 2
                 ? [
                     {

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

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

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