react-msaview 5.0.7 → 5.0.13

package/dist/components/Checkbox2.js

@@ -1,10 +1,7 @@
 import React from 'react';
-import { Checkbox, FormControlLabel, } from '@mui/material';
-function FormControlLabel2(rest) {
-    return (React.createElement("div", null,
-        React.createElement(FormControlLabel, { ...rest })));
-}
+import { Checkbox, FormControlLabel } from '@mui/material';
 export default function Checkbox2({ checked, label, disabled, onChange, }) {
-    return (React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { disabled: disabled, checked: checked, onChange: onChange }), label: label }));
+    return (React.createElement("div", null,
+        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { disabled: disabled, checked: checked, onChange: onChange }), label: label })));
 }
 //# sourceMappingURL=Checkbox2.js.map

package/dist/components/Checkbox2.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Checkbox2.js","sourceRoot":"","sources":["../../src/components/Checkbox2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAA;AAE1D,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,EAChC,OAAO,EACP,KAAK,EACL,QAAQ,EACR,QAAQ,GAMT;IACC,OAAO,CACL;QACE,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IAAC,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,QAAQ,GAAI,EAExE,KAAK,EAAE,KAAK,GACZ,CACE,CACP,CAAA;AACH,CAAC"}

package/dist/components/MSAViewer.d.ts

@@ -0,0 +1,14 @@
+import React from 'react';
+import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
+interface MSAViewerProps {
+    msa?: string;
+    tree?: string;
+    gff?: string;
+    msaFilehandle?: FileLocationType;
+    treeFilehandle?: FileLocationType;
+    gffFilehandle?: FileLocationType;
+    colorScheme?: string;
+    height?: number;
+}
+export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, }: MSAViewerProps): React.JSX.Element;
+export {};

package/dist/components/MSAViewer.js

@@ -0,0 +1,34 @@
+import React, { useEffect, useMemo } from 'react';
+import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
+import useMeasure from '@jbrowse/core/util/useMeasure';
+import { ThemeProvider } from '@mui/material/styles';
+import MSAModelF from "../model.js";
+import Loading from "./Loading.js";
+export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, }) {
+    const theme = useMemo(() => createJBrowseTheme(), []);
+    const model = useMemo(() => MSAModelF().create({
+        type: 'MsaView',
+        ...(msa || tree || gff
+            ? { data: { msa: msa ?? '', tree: tree ?? '', gff } }
+            : {}),
+        ...(msaFilehandle ? { msaFilehandle } : {}),
+        ...(treeFilehandle ? { treeFilehandle } : {}),
+        ...(gffFilehandle ? { gffFilehandle } : {}),
+        ...(colorScheme ? { colorSchemeName: colorScheme } : {}),
+        ...(height ? { height } : {}),
+    }), 
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+    []);
+    const [ref, { width }] = useMeasure();
+    useEffect(() => {
+        if (width) {
+            requestAnimationFrame(() => {
+                model.setWidth(width);
+            });
+        }
+    }, [model, width]);
+    return (React.createElement(ThemeProvider, { theme: theme },
+        React.createElement("div", { ref: ref },
+            React.createElement(Loading, { model: model }))));
+}
+//# sourceMappingURL=MSAViewer.js.map

package/dist/components/MSAViewer.js.map

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

@@ -1,8 +1,9 @@
-import React, { lazy, useEffect, useRef, useState } from 'react';
+import React, { lazy, useCallback, useRef, useState } from 'react';
 import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
 import { IconButton, Menu, MenuItem } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
+import { useWheelScroll } from "../useWheelScroll.js";
 const TrackInfoDialog = lazy(() => import("./dialogs/TrackInfoDialog.js"));
 const useStyles = makeStyles()({
     button: {
@@ -50,30 +51,10 @@ const Track = observer(function ({ model, track, }) {
     const { resizeHandleWidth, colWidth, scrollX, numColumns } = model;
     const { model: { height, error }, } = track;
     const ref = useRef(null);
-    const scheduled = useRef(false);
-    const deltaX = useRef(0);
-    useEffect(() => {
-        const curr = ref.current;
-        if (!curr) {
-            return;
-        }
-        function onWheel(event) {
-            deltaX.current += event.deltaX;
-            if (!scheduled.current) {
-                scheduled.current = true;
-                requestAnimationFrame(() => {
-                    model.doScrollX(-deltaX.current);
-                    deltaX.current = 0;
-                    scheduled.current = false;
-                });
-            }
-            event.preventDefault();
-        }
-        curr.addEventListener('wheel', onWheel, { passive: false });
-        return () => {
-            curr.removeEventListener('wheel', onWheel);
-        };
+    const onScrollX = useCallback((d) => {
+        model.doScrollX(d);
     }, [model]);
+    useWheelScroll({ ref, onScrollX });
     return (React.createElement("div", { key: track.id, style: { display: 'flex', height } },
         React.createElement(TrackLabel, { model: model, track: track }),
         React.createElement("div", { style: { width: resizeHandleWidth, flexShrink: 0 } }),

package/dist/components/Track.js.map

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package/dist/components/dialogs/DomainDialog.js

@@ -2,7 +2,6 @@ import React, { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { Tab, Tabs } from '@mui/material';
 import InterProScanPanel from "./InterProScanDialog.js";
-import TabPanel from "./TabPanel.js";
 import UserProvidedResultPanel from "./UserProvidedDomainsDialog.js";
 export default function LaunchDomainViewDialog({ handleClose, model, }) {
     const [choice, setChoice] = useState(0);
@@ -14,9 +13,7 @@ export default function LaunchDomainViewDialog({ handleClose, model, }) {
             } },
             React.createElement(Tab, { value: 0, label: "Automatic lookup" }),
             React.createElement(Tab, { value: 1, label: "Manual" })),
-        React.createElement(TabPanel, { value: choice, index: 0 },
-            React.createElement(InterProScanPanel, { model: model, handleClose: handleClose })),
-        React.createElement(TabPanel, { value: choice, index: 1 },
-            React.createElement(UserProvidedResultPanel, { model: model, handleClose: handleClose }))));
+        choice === 0 ? (React.createElement(InterProScanPanel, { model: model, handleClose: handleClose })) : null,
+        choice === 1 ? (React.createElement(UserProvidedResultPanel, { model: model, handleClose: handleClose })) : null));
 }
 //# sourceMappingURL=DomainDialog.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"DomainDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/DomainDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAEzC,OAAO,iBAAiB,MAAM,yBAA0B,CAAA;AACxD,OAAO,uBAAuB,MAAM,gCAAiC,CAAA;AAIrE,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAAC,EAC7C,WAAW,EACX,KAAK,GAIN;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACvC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,qBAAqB,EAC3B,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC,EACD,IAAI;QAEJ,oBAAC,IAAI,IACH,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;gBACnB,SAAS,CAAC,GAAG,CAAC,CAAA;YAChB,CAAC;YAED,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,kBAAkB,GAAG;YAC1C,oBAAC,GAAG,IAAC,KAAK,EAAE,CAAC,EAAE,KAAK,EAAC,QAAQ,GAAG,CAC3B;QACN,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CACd,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,WAAW,GAAI,CAC9D,CAAC,CAAC,CAAC,IAAI;QACP,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CACd,oBAAC,uBAAuB,IAAC,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,WAAW,GAAI,CACpE,CAAC,CAAC,CAAC,IAAI,CACD,CACV,CAAA;AACH,CAAC"}

package/dist/components/dialogs/InterProScanDialog.js

@@ -45,32 +45,32 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
             category: 'Other category',
         },
         {
-            name: 'SUPERFAMILY',
+            name: 'SuperFamily',
             category: 'Structural domains',
             checked: true,
         },
         {
-            name: 'PANTHER',
+            name: 'Panther',
             category: 'Families, domains, sites & repeats',
             checked: true,
         },
         {
-            name: 'Gene3D',
+            name: 'Gene3d',
             category: 'Structural domains',
             checked: true,
         },
         {
-            name: 'Hamap',
+            name: 'HAMAP',
             category: 'Families, domains, sites & repeats',
             checked: true,
         },
         {
-            name: 'ProSiteProfiles',
+            name: 'PrositeProfiles',
             category: 'Families, domains, sites & repeats',
             checked: true,
         },
         {
-            name: 'ProSitePatterns',
+            name: 'PrositePatterns',
             category: 'Families, domains, sites & repeats',
             checked: true,
         },
@@ -96,7 +96,7 @@ const InterProScanDialog = observer(function ({ handleClose, model, }) {
             checked: true,
         },
         {
-            name: 'Pfam',
+            name: 'PfamA',
             category: 'Families, domains, sites & repeats',
             checked: true,
         },

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

@@ -1 +1 @@
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+{"version":3,"file":"InterProScanDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/InterProScanDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAA;AAIhE,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,WAAW,EACX,KAAK,GAIN;IACC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC;QAC/B;YACE,IAAI,EAAE,SAAS;YACf,WAAW,EAAE,qCAAqC;YAClD,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,MAAM;YACZ,WAAW,EAAE,qCAAqC;YAClD,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,IAAI;YACb,WAAW,EACT,gEAAgE;YAClE,QAAQ,EAAE,yBAAyB;SACpC;QACD;YACE,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,yBAAyB;SACpC;QACD;YACE,IAAI,EAAE,aAAa;YACnB,QAAQ,EAAE,gBAAgB;YAC1B,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,uBAAuB;YAC7B,QAAQ,EAAE,gBAAgB;YAC1B,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,uBAAuB;YAC7B,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,gBAAgB;SAC3B;QACD;YACE,IAAI,EAAE,aAAa;YACnB,QAAQ,EAAE,oBAAoB;YAC9B,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,QAAQ;YACd,QAAQ,EAAE,oBAAoB;YAC9B,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,iBAAiB;YACvB,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,iBAAiB;YACvB,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,yBAAyB;YACnC,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,KAAK;YACX,WAAW,EAAE,4BAA4B;YACzC,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,QAAQ;YACd,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,oCAAoC;YAC9C,OAAO,EAAE,IAAI;SACd;QACD;YACE,IAAI,EAAE,YAAY;YAClB,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,yBAAyB;SACpC;QACD;YACE,IAAI,EAAE,OAAO;YACb,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,gBAAgB;SAC3B;QACD;YACE,IAAI,EAAE,OAAO;YACb,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,yBAAyB;SACpC;QAED;YACE,IAAI,EAAE,SAAS;YACf,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,gBAAgB;SAC3B;QACD;YACE,IAAI,EAAE,QAAQ;YACd,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,gBAAgB;SAC3B;QACD;YACE,IAAI,EAAE,OAAO;YACb,OAAO,EAAE,IAAI;YACb,QAAQ,EAAE,oCAAoC;SAC/C;KACF,CAAC,CAAA;IAEF,MAAM,QAAQ,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC7D,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvC,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,oCAAoC,EAC1C,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;QACf,CAAC,EACD,IAAI;QAEJ,oBAAC,aAAa;YACZ,oBAAC,UAAU,6FAGE;YACb,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,OAAO,CAAC,CAAC,IAAI,CAAC,CAAA;gBAChB,CAAC;gBAEA,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM;oCAChB;YACR,IAAI,CAAC,CAAC,CAAC,CACN;gBACE,oBAAC,UAAU,oDAAuD;gBAClE;oBACE,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;4BACZ,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;wBACpD,CAAC,kBAGM;oBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;4BACZ,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;wBACnD,CAAC,iBAGM,CACL;gBACN;oBACE,mCACG,IAAI;yBACF,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC;yBACxD,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC,CACpC,4BAAI,GAAG,EAAE,IAAI;wBACX;4BACE,+BACE,IAAI,EAAC,UAAU,EACf,GAAG,EAAE,IAAI,EACT,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,GAAG,EAAE;oCACb,OAAO,CACL,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CACX,CAAC,CAAC,IAAI,KAAK,IAAI;wCACb,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,OAAO,EAAE;wCAC/B,CAAC,CAAC,CAAC,CACN,CACF,CAAA;gCACH,CAAC,GACD,CACC;wBACL,gCAAK,IAAI,CAAM;wBACf,gCAAK,QAAQ,CAAM,CAChB,CACN,CAAC,CACE,CACF,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACM;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,CAAC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;4BACtB,IAAI,IAAI,CAAC,MAAM,GAAG,GAAG,EAAE,CAAC;gCACtB,MAAM,IAAI,KAAK,CACb,qDAAqD,CACtD,CAAA;4BACH,CAAC;4BACD,MAAM,kBAAkB,CAAC;gCACvB,SAAS,EAAE,cAAc;gCACzB,QAAQ,EAAE,QAAQ;gCAClB,GAAG,EAAE,IAAI;qCACN,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC;qCAChD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;qCACnB,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;qCACnC,IAAI,CAAC,IAAI,CAAC;gCACb,UAAU,EAAE,GAAG,CAAC,EAAE;oCAChB,KA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package/dist/components/dialogs/SettingsDialog.js

@@ -23,8 +23,7 @@ const SettingsContent = observer(function ({ model }) {
         React.createElement(MSASettings, { model: model })));
 });
 const TreeSettings = observer(function TreeSettings({ model, }) {
-    const { classes } = useStyles();
-    const { drawTree, drawLabels, drawNodeBubbles, labelsAlignRight, noTree, showBranchLen, treeWidthMatchesArea, treeWidth, } = model;
+    const { drawTree, drawLabels, drawNodeBubbles, labelsAlignRight, showBranchLen, } = model;
     return (React.createElement("div", null,
         React.createElement("h1", null, "Tree options"),
         React.createElement(Checkbox2, { checked: showBranchLen, label: "Show branch length?", onChange: () => {
@@ -41,23 +40,11 @@ const TreeSettings = observer(function TreeSettings({ model, }) {
             } }),
         React.createElement(Checkbox2, { checked: drawLabels, label: "Draw labels", onChange: () => {
                 model.setDrawLabels(!drawLabels);
-            } }),
-        noTree ? null : (React.createElement("div", null,
-            React.createElement(Checkbox2, { checked: treeWidthMatchesArea, label: "Make tree width fit to tree area?", onChange: () => {
-                    model.setTreeWidthMatchesArea(!treeWidthMatchesArea);
-                } }),
-            treeWidthMatchesArea ? null : (React.createElement("div", { className: classes.flex },
-                React.createElement(Typography, null,
-                    "Tree width (",
-                    treeWidth,
-                    "px)"),
-                React.createElement(Slider, { className: classes.field, min: 50, max: 600, value: treeWidth, onChange: (_, val) => {
-                        model.setTreeWidth(val);
-                    } })))))));
+            } })));
 });
 const MSASettings = observer(function MSASettings({ model, }) {
     const { classes } = useStyles();
-    const { bgColor, contrastLettering, colWidth, allowedGappyness, drawMsaLetters, colorSchemeName, hideGaps, rowHeight, } = model;
+    const { bgColor, colWidth, allowedGappyness, drawMsaLetters, colorSchemeName, hideGaps, rowHeight, } = model;
     return (React.createElement("div", null,
         React.createElement("h1", null, "MSA options"),
         React.createElement(Checkbox2, { checked: drawMsaLetters, label: "Draw letters", onChange: () => {
@@ -66,9 +53,6 @@ const MSASettings = observer(function MSASettings({ model, }) {
         React.createElement(Checkbox2, { checked: bgColor, label: "Color letters instead of background of tiles", onChange: () => {
                 model.setBgColor(!bgColor);
             } }),
-        React.createElement(Checkbox2, { checked: contrastLettering, label: "Use contrast lettering", onChange: () => {
-                model.setContrastLettering(!contrastLettering);
-            } }),
         React.createElement(Checkbox2, { checked: hideGaps, label: "Enable hiding gappy columns?", onChange: () => {
                 model.setHideGaps(!hideGaps);
             } }),

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

@@ -1 +1 @@
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+{"version":3,"file":"SettingsDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/SettingsDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,QAAQ,EACR,MAAM,EACN,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,YAAY,MAAM,uBAAuB,CAAA;AAChD,OAAO,SAAS,MAAM,iBAAkB,CAAA;AAIxC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;IACD,IAAI,EAAE;QACJ,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AAEpC,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC3E,OAAO,CACL;QACE,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,GAAI,CAC5B,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,YAAY,CAAC,EAClD,KAAK,GAGN;IACC,MAAM,EACJ,QAAQ,EACR,UAAU,EACV,eAAe,EACf,gBAAgB,EAChB,aAAa,GACd,GAAG,KAAK,CAAA;IAET,OAAO,CACL;QACE,+CAAqB;QACrB,oBAAC,SAAS,IACR,OAAO,EAAE,aAAa,EACtB,KAAK,EAAC,qBAAqB,EAC3B,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;YACxC,CAAC,GACD;QAEF,oBAAC,SAAS,IACR,OAAO,EAAE,eAAe,EACxB,KAAK,EAAC,0CAA0C,EAChD,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC,CAAA;YAC5C,CAAC,GACD;QACF,oBAAC,SAAS,IACR,OAAO,EAAE,QAAQ,EACjB,KAAK,EAAC,YAAY,EAClB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;YAC9B,CAAC,GACD;QAEF,oBAAC,SAAS,IACR,OAAO,EAAE,gBAAgB,EACzB,KAAK,EAAC,0BAA0B,EAChC,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,mBAAmB,CAAC,CAAC,gBAAgB,CAAC,CAAA;YAC9C,CAAC,GACD;QAEF,oBAAC,SAAS,IACR,OAAO,EAAE,UAAU,EACnB,KAAK,EAAC,aAAa,EACnB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,aAAa,CAAC,CAAC,UAAU,CAAC,CAAA;YAClC,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,WAAW,CAAC,EAChD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EACJ,OAAO,EACP,QAAQ,EACR,gBAAgB,EAChB,cAAc,EACd,eAAe,EACf,QAAQ,EACR,SAAS,GACV,GAAG,KAAK,CAAA;IAET,OAAO,CACL;QACE,8CAAoB;QACpB,oBAAC,SAAS,IACR,OAAO,EAAE,cAAc,EACvB,KAAK,EAAC,cAAc,EACpB,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;YAC1C,CAAC,GACD;QACF,oBAAC,SAAS,IACR,OAAO,EAAE,OAAO,EAChB,KAAK,EAAC,8CAA8C,EACpD,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,UAAU,CAAC,CAAC,OAAO,CAAC,CAAA;YAC5B,CAAC,GACD;QACF,oBAAC,SAAS,IACR,OAAO,EAAE,QAAQ,EACjB,KAAK,EAAC,8BAA8B,EACpC,QAAQ,EAAE,GAAG,EAAE;gBACb,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;YAC9B,CAAC,GACD;QACD,QAAQ,CAAC,CAAC,CAAC,CACV,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU;;gBAAsB,gBAAgB;yBAAoB;YACrE,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,gBAAgB,EACvB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;oBACnB,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;gBAChC,CAAC,GACD,CACE,CACP,CAAC,CAAC,CAAC,IAAI;QACR,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU;;gBAAgB,GAAG,CAAC,QAAQ,CAAC;sBAAiB;YACzD,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,EAAE,EACP,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;oBACnB,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;gBACxB,CAAC,GACD,CACE;QACN,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU;;gBAAc,GAAG,CAAC,SAAS,CAAC;sBAAiB;YACxD,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,EAAE,EACP,KAAK,EAAE,SAAS,EAChB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;oBACnB,KAAK,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;gBACzB,CAAC,GACD,CACE;QAEN,oBAAC,SAAS,IACR,MAAM,QACN,KAAK,EAAC,cAAc,EACpB,KAAK,EAAE,eAAe,EACtB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,KAAK,CAAC,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAC9C,CAAC,IAEA,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CACvC,oBAAC,QAAQ,IAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,IACjC,MAAM,CACE,CACZ,CAAC,CACQ,CACR,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,KAAK,EAAC,UAAU,EAChB,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;QAED,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;YACjC,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,OAAO,EAAE,CAAA;oBACX,CAAC,aAGM,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

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

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

package/dist/components/header/ColorSchemeMenu.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.js";
+const ColorSchemeMenu = observer(function ({ model }) {
+    const { colorSchemeName } = model;
+    return (React.createElement(CascadingMenuButton, { closeAfterItemClick: true, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: Object.keys(colorSchemes).map(option => ({
+            label: option,
+            type: 'radio',
+            checked: colorSchemeName === option,
+            onClick: () => {
+                model.setColorSchemeName(option);
+            },
+        })) },
+        React.createElement(Palette, null)));
+});
+export default ColorSchemeMenu;
+//# sourceMappingURL=ColorSchemeMenu.js.map

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

@@ -0,0 +1 @@
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package/dist/components/header/{ZoomStar.d.ts → FileMenu.d.ts}

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

package/dist/components/header/FileMenu.js

@@ -0,0 +1,71 @@
+import React, { lazy } from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import Assignment from '@mui/icons-material/Assignment';
+import FolderOpen from '@mui/icons-material/FolderOpen';
+import PhotoCamera from '@mui/icons-material/PhotoCamera';
+import Settings from '@mui/icons-material/Settings';
+import { observer } from 'mobx-react';
+import { getDomainMenu } from "./getDomainsMenu.js";
+const MetadataDialog = lazy(() => import("../dialogs/MetadataDialog.js"));
+const ExportSVGDialog = lazy(() => import("../dialogs/ExportSVGDialog.js"));
+const SettingsDialog = lazy(() => import("../dialogs/SettingsDialog.js"));
+const FileMenu = observer(({ model }) => {
+    return (React.createElement(CascadingMenuButton, { menuItems: [
+            {
+                label: 'Return to import form',
+                icon: FolderOpen,
+                onClick: () => {
+                    model.reset();
+                },
+            },
+            {
+                label: 'Metadata',
+                icon: Assignment,
+                onClick: () => {
+                    model.queueDialog(onClose => [
+                        MetadataDialog,
+                        {
+                            model,
+                            onClose,
+                        },
+                    ]);
+                },
+            },
+            {
+                label: 'More settings',
+                icon: Settings,
+                onClick: () => {
+                    model.queueDialog(onClose => [
+                        SettingsDialog,
+                        {
+                            model,
+                            onClose,
+                        },
+                    ]);
+                },
+            },
+            {
+                label: 'Domain settings',
+                type: 'subMenu',
+                subMenu: getDomainMenu({
+                    model,
+                }),
+            },
+            {
+                label: 'Export SVG',
+                icon: PhotoCamera,
+                onClick: () => {
+                    model.queueDialog(onClose => [
+                        ExportSVGDialog,
+                        {
+                            onClose,
+                            model,
+                        },
+                    ]);
+                },
+            },
+        ], anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' } },
+        React.createElement(FolderOpen, null)));
+});
+export default FileMenu;
+//# sourceMappingURL=FileMenu.js.map

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

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

@@ -3,15 +3,16 @@ 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 ColorSchemeMenu from "./ColorSchemeMenu.js";
+import FileMenu from "./FileMenu.js";
 import GappynessSlider from "./GappynessSlider.js";
 import HeaderInfoArea from "./HeaderInfoArea.js";
-import HeaderMenu from "./HeaderMenu.js";
 import HeaderStatusArea from "./HeaderStatusArea.js";
+import MSASettingsMenu from "./MSASettingsMenu.js";
 import MultiAlignmentSelector from "./MultiAlignmentSelector.js";
-import SettingsMenu from "./SettingsMenu.js";
+import TreeSettingsMenu from "./TreeSettingsMenu.js";
 import ZoomControls from "./ZoomControls.js";
 import ZoomMenu from "./ZoomMenu.js";
-import ZoomStar from "./ZoomStar.js";
 const AboutDialog = lazy(() => import("../dialogs/AboutDialog.js"));
 const Header = observer(function ({ model }) {
     const [ref, { height }] = useMeasure();
@@ -19,10 +20,11 @@ const Header = observer(function ({ model }) {
         model.setHeaderHeight(height || 0);
     }, [model, height]);
     return (React.createElement("div", { ref: ref, style: { display: 'flex' } },
-        React.createElement(HeaderMenu, { model: model }),
-        React.createElement(SettingsMenu, { model: model }),
+        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 }),
-        model.showZoomStar ? React.createElement(ZoomStar, { model: model }) : null,
         React.createElement(ZoomMenu, { model: model }),
         React.createElement(GappynessSlider, { model: model }),
         React.createElement("div", { style: { paddingLeft: 20, margin: 'auto' } },

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

@@ -1 +1 @@
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