react-msaview 3.1.10 → 3.1.12

package/dist/parsers/StockholmMSA.d.ts

@@ -24,8 +24,8 @@ export default class StockholmMSA {
     get alignmentNames(): string[];
     getHeader(): {
         General: {
-            DE?: string[] | undefined;
-            NH?: string[] | undefined;
+            DE?: string[];
+            NH?: string[];
         };
         Accessions: Record<string, string>;
         Dbxref: Record<string, string>;

package/dist/renderToSvg.js

@@ -44,29 +44,6 @@ async function render({ width, height, offsetX, offsetY, theme, model, includeMi
         React.createElement(Wrapper, { model: model },
             React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, width: width, height: height }))), createRoot);
 }
-// function renderMultiline({ model }: { model: MsaViewModel }) {
-//   const { treeAreaWidth, height } = model
-//   const clipId = 'tree'
-//   return (
-//     <Wrapper model={model}>
-//       <defs>
-//         <clipPath id={clipId}>
-//           <rect x={0} y={0} width={treeAreaWidth} height={height} />
-//         </clipPath>
-//       </defs>
-//       <g
-//         clipPath={`url(#${clipId})`}
-//         /* eslint-disable-next-line react/no-danger */
-//         dangerouslySetInnerHTML={{ __html: ctx1.getSvg().innerHTML }}
-//       />
-//       <g
-//         transform={`translate(${treeAreaWidth} 0)`}
-//         /* eslint-disable-next-line react/no-danger */
-//         dangerouslySetInnerHTML={{ __html: ctx2.getSvg().innerHTML }}
-//       />
-//     </Wrapper>
-//   )
-// }
 function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context, }) {
     const clipId1 = 'tree';
     const clipId2 = 'msa';

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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+{"version":3,"file":"renderToSvg.js","sourceRoot":"","sources":["../src/renderToSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAA;AAC7C,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAKzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAA;AAChE,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAA;AAEtC,OAAO,UAAU,MAAM,iCAAiC,CAAA;AACxD,OAAO,EAAE,2BAA2B,EAAE,MAAM,8CAA8C,CAAA;AAE1F,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,KAAmB,EACnB,IAAoE;IAEpE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACrC,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACjD,MAAM,EAAE,UAAU,EAAE,KAAK,EAAE,cAAc,EAAE,GAAG,IAAI,CAAA;IAElD,IAAI,UAAU,KAAK,QAAQ,EAAE,CAAC;QAC5B,OAAO,MAAM,CAAC;YACZ,KAAK,EAAE,KAAK,CAAC,UAAU,GAAG,KAAK,CAAC,aAAa;YAC7C,MAAM,EAAE,KAAK,CAAC,WAAW;YACzB,KAAK;YACL,KAAK;YACL,OAAO,EAAE,CAAC;YACV,OAAO,EAAE,CAAC;YACV,cAAc;SACf,CAAC,CAAA;IACJ,CAAC;SAAM,IAAI,UAAU,KAAK,UAAU,EAAE,CAAC;QACrC,OAAO,MAAM,CAAC;YACZ,KAAK;YACL,MAAM;YACN,KAAK;YACL,KAAK;YACL,OAAO,EAAE,OAAO;YAChB,OAAO,EAAE,CAAC,OAAO;YACjB,cAAc;SACf,CAAC,CAAA;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;AACH,CAAC;AAED,KAAK,UAAU,MAAM,CAAC,EACpB,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,KAAK,EACL,KAAK,EACL,cAAc,GASf;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,OAAO,GAAG,cAAc,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,WAAW,CAAA;IAE7D,OAAO,oBAAoB,CACzB,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM;QACtC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK;YACnB,oBAAC,aAAa,IACZ,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,GACd,CACM,CACC,EACb,UAAU,CACX,CAAA;AACH,CAAC;AAED,SAAS,aAAa,CAAC,EACrB,KAAK,EACL,KAAK,EACL,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,OAAO,GAYR;IACC,MAAM,OAAO,GAAG,MAAM,CAAA;IACtB,MAAM,OAAO,GAAG,KAAK,CAAA;IACrB,MAAM,EAAE,aAAa,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,cAAc,GAAG,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC,CAAA;IACxD,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACnC,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACnC,2BAA2B,CAAC;QAC1B,GAAG,EAAE,IAAI;QACT,OAAO;QACP,OAAO;QACP,KAAK;QACL,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,MAAM,YAAY,GAAG,KAAK,GAAG,aAAa,CAAA;IAC1C,gBAAgB,CAAC;QACf,KAAK;QACL,OAAO;QACP,GAAG,EAAE,IAAI;QACT,KAAK;QACL,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,cAAc,CAAC;QACb,KAAK;QACL,KAAK;QACL,OAAO;QACP,OAAO;QACP,cAAc;QACd,GAAG,EAAE,IAAI;QACT,kBAAkB,EAAE,YAAY;QAChC,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,OAAO;gBACnB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,MAAM,EAAE,MAAM,GAAI,CACjD,CACN;QACP;YACE,kCAAU,EAAE,EAAE,OAAO;gBACnB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,GAAI,CAChD,CACN;QAEP,2BACE,QAAQ,EAAE,QAAQ,OAAO,GAAG;YAC5B,8CAA8C;YAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D;QACF,2BACE,QAAQ,EAAE,QAAQ,OAAO,GAAG,EAC5B,SAAS,EAAE,aAAa,aAAa,KAAK;YAC1C,8CAA8C;YAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,EACtB,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAE9C,OAAO,CACL;QACE,2BAAG,SAAS,EAAE,aAAa,aAAa,KAAK;YAC3C,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B;QAEJ,2BAAG,SAAS,EAAE,eAAe,aAAa,GAAG,IAAG,QAAQ,CAAK,CAC5D,CACJ,CAAA;AACH,CAAC;AAED,SAAS,UAAU,CAAC,EAClB,KAAK,EACL,MAAM,EACN,QAAQ,GAKT;IACC,OAAO,CACL,6BACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAC,4BAA4B,EAClC,UAAU,EAAC,8BAA8B,EACzC,OAAO,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,QAAQ,EAAE,IAExC,QAAQ,CACL,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EAAE,QAAQ,EAAiC;IAC9D,OAAO,QAAQ,CAAA;AACjB,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.1.10";
+export declare const version = "3.1.12";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.10';
+export const version = '3.1.12';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.10",
+  "version": "3.1.12",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",
@@ -16,7 +16,6 @@
   "scripts": {
     "clean": "rimraf dist",
     "prebuild": "npm run clean",
-    "test": "jest",
     "prepublishOnly": "node output-version.js > src/version.ts && git add -A src && git commit -m '[skip ci] Bump version.ts'",
     "build:esm": "tsc",
     "build:bundle": "rollup -c --bundleConfigAsCjs",
@@ -43,10 +42,8 @@
     "d3-array": "^3.2.3",
     "d3-hierarchy": "^3.1.2",
     "file-saver": "^2.0.5",
-    "normalize-wheel": "^1.0.1",
     "rbush": "^3.0.1",
     "react-error-boundary": "^4.0.13",
-    "rollup": "^4.9.1",
     "stockholm-js": "^1.0.10",
     "svgcanvas": "^2.5.0"
   }

package/src/components/Loading.tsx

@@ -28,12 +28,14 @@ const Loading = observer(function ({ model }: { model: MsaViewModel }) {
       <ErrorBoundary
         fallbackRender={props => <Reset model={model} error={props.error} />}
       >
-        {!initialized ? (
-          <ImportForm model={model} />
-        ) : isLoading ? (
-          <Typography variant="h4">Loading...</Typography>
+        {initialized ? (
+          isLoading ? (
+            <Typography variant="h4">Loading...</Typography>
+          ) : (
+            <MSAView model={model} />
+          )
         ) : (
-          <MSAView model={model} />
+          <ImportForm model={model} />
         )}
       </ErrorBoundary>
     </div>

package/src/components/SequenceTextArea.tsx

@@ -9,6 +9,7 @@ import Checkbox2 from './Checkbox2'
 const useStyles = makeStyles()({
   textAreaFont: {
     fontFamily: 'Courier New',
+    wordWrap: 'break-word',
   },
   dialogContent: {
     background: 'lightgrey',
@@ -21,8 +22,11 @@ export default function SequenceTextArea({ str }: { str: [string, string][] }) {
   const { classes } = useStyles()
   const [copied, setCopied] = useState(false)
   const [showGaps, setShowGaps] = useState(false)
+  const [showEmpty, setShowEmpty] = useState(false)
 
   const disp = str
+    .map(([s1, s2]) => [s1, showGaps ? s2 : s2.replaceAll('-', '')])
+    .filter(f => (showEmpty ? true : !!f[1]))
     .map(([s1, s2]) => `>${s1}\n${showGaps ? s2 : s2.replaceAll('-', '')}`)
     .join('\n')
   return (
@@ -43,6 +47,11 @@ export default function SequenceTextArea({ str }: { str: [string, string][] }) {
         checked={showGaps}
         onChange={() => setShowGaps(!showGaps)}
       />
+      <Checkbox2
+        label="Show empty"
+        checked={showEmpty}
+        onChange={() => setShowEmpty(!showEmpty)}
+      />
       <TextField
         variant="outlined"
         multiline

package/src/components/dialogs/DomainDialog.tsx

@@ -0,0 +1,38 @@
+import React, { useState } from 'react'
+import { Dialog } from '@jbrowse/core/ui'
+import { Tab, Tabs } from '@mui/material'
+
+// locals
+import InterProScanPanel from './InterProScanPanel'
+import UserProvidedResultPanel from './UserProvidedResultPanel'
+import TabPanel from './TabPanel'
+import { MsaViewModel } from '../../model'
+
+export default function LaunchDomainViewDialog({
+  handleClose,
+  model,
+}: {
+  handleClose: () => void
+  model: MsaViewModel
+}) {
+  const [choice, setChoice] = useState(0)
+  return (
+    <Dialog
+      maxWidth="xl"
+      title="Launch protein view"
+      onClose={() => handleClose()}
+      open
+    >
+      <Tabs value={choice} onChange={(_, val) => setChoice(val)}>
+        <Tab value={0} label="Automatic lookup" />
+        <Tab value={1} label="Manual" />
+      </Tabs>
+      <TabPanel value={choice} index={0}>
+        <InterProScanPanel model={model} handleClose={handleClose} />
+      </TabPanel>
+      <TabPanel value={choice} index={1}>
+        <UserProvidedResultPanel model={model} handleClose={handleClose} />
+      </TabPanel>
+    </Dialog>
+  )
+}

package/src/components/dialogs/{InterProScanDialog.tsx → InterProScanPanel.tsx}

@@ -1,16 +1,17 @@
 import React, { useState } from 'react'
 import { observer } from 'mobx-react'
-import { Dialog } from '@jbrowse/core/ui'
 import { Button, DialogActions, DialogContent, Typography } from '@mui/material'
 
 // locals
 import { MsaViewModel } from '../../model'
+import { getSession } from '@jbrowse/core/util'
+import { launchInterProScan } from '../../launchInterProScan'
 
-const FeatureTypeDialog = observer(function ({
-  onClose,
+const InterProScanDialog = observer(function ({
+  handleClose,
   model,
 }: {
-  onClose: () => void
+  handleClose: () => void
   model: MsaViewModel
 }) {
   const [vals, setVals] = useState([
@@ -146,7 +147,7 @@ const FeatureTypeDialog = observer(function ({
   const [show, setShow] = useState(false)
 
   return (
-    <Dialog onClose={() => onClose()} open title="Feature types" maxWidth="xl">
+    <>
       <DialogContent>
         <Typography>
           This will run InterProScan on all rows of the current MSA
@@ -209,22 +210,52 @@ const FeatureTypeDialog = observer(function ({
         ) : null}
       </DialogContent>
       <DialogActions>
-        <Button variant="contained" color="secondary" onClick={() => onClose()}>
+        <Button
+          variant="contained"
+          color="secondary"
+          onClick={() => handleClose()}
+        >
           Cancel
         </Button>
         <Button
           variant="contained"
           color="primary"
           onClick={() => {
-            model.queryInterProScan(programs).catch(e => model.setError(e))
-            onClose()
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            ;(async () => {
+              try {
+                const { rows } = model
+                if (rows.length > 140) {
+                  throw new Error(
+                    'Too many sequences, please run InterProScan offline',
+                  )
+                }
+                await launchInterProScan({
+                  algorithm: 'interproscan',
+                  programs: programs,
+                  seq: rows
+                    .map(row => [row[0], row[1].replaceAll('-', '')])
+                    .filter(f => !!f[1])
+                    .map(row => `>${row[0]}\n${row[1]}`)
+                    .join('\n'),
+                  onProgress: arg => model.setStatus(arg),
+                  model,
+                })
+              } catch (e) {
+                console.error(e)
+                getSession(model).notifyError(`${e}`, e)
+              } finally {
+                model.setStatus()
+              }
+            })()
+            handleClose()
           }}
         >
           Send sequences to InterProScan
         </Button>
       </DialogActions>
-    </Dialog>
+    </>
   )
 })
 
-export default FeatureTypeDialog
+export default InterProScanDialog

package/src/components/dialogs/SettingsDialog.tsx

@@ -82,7 +82,7 @@ const TreeSettings = observer(function TreeSettings({
         onChange={() => model.setDrawLabels(!drawLabels)}
         label="Draw labels"
       />
-      {!noTree ? (
+      {noTree ? null : (
         <div>
           <Checkbox2
             checked={treeWidthMatchesArea}
@@ -91,7 +91,7 @@ const TreeSettings = observer(function TreeSettings({
             }
             label="Make tree width fit to tree area?"
           />
-          {!treeWidthMatchesArea ? (
+          {treeWidthMatchesArea ? null : (
             <div className={classes.flex}>
               <Typography>Tree width ({treeWidth}px)</Typography>
               <Slider
@@ -102,9 +102,9 @@ const TreeSettings = observer(function TreeSettings({
                 onChange={(_, val) => model.setTreeWidth(val as number)}
               />
             </div>
-          ) : null}
+          )}
         </div>
-      ) : null}
+      )}
     </div>
   )
 })

package/src/components/dialogs/TabPanel.tsx

@@ -0,0 +1,19 @@
+import React from 'react'
+
+// this is from MUI example
+export default function TabPanel({
+  children,
+  value,
+  index,
+  ...other
+}: {
+  children?: React.ReactNode
+  index: number
+  value: number
+}) {
+  return (
+    <div role="tabpanel" hidden={value !== index} {...other}>
+      {value === index && <div>{children}</div>}
+    </div>
+  )
+}

package/src/components/dialogs/UserProvidedResultPanel.tsx

@@ -0,0 +1,119 @@
+import React, { useState } from 'react'
+import { observer } from 'mobx-react'
+import {
+  Button,
+  DialogActions,
+  DialogContent,
+  FormControlLabel,
+  FormControl,
+  Radio,
+  RadioGroup,
+  TextField,
+  Typography,
+} from '@mui/material'
+import { getSession } from '@jbrowse/core/util'
+
+// locals
+import { MsaViewModel } from '../../model'
+import { jsonfetch } from '../../fetchUtils'
+import { InterProScanResponse } from '../../launchInterProScan'
+
+const FeatureTypeDialog = observer(function ({
+  handleClose,
+  model,
+}: {
+  handleClose: () => void
+  model: MsaViewModel
+}) {
+  const [file, setFile] = useState<File>()
+  const [choice, setChoice] = useState('file')
+  const [interProURL, setInterProURL] = useState('')
+
+  return (
+    <>
+      <DialogContent>
+        <div style={{ display: 'flex', margin: 30 }}>
+          <Typography>
+            Open a JSON file of InterProScan results that you run remotely on
+            EBI servers or locally
+          </Typography>
+
+          <FormControl component="fieldset">
+            <RadioGroup
+              value={choice}
+              onChange={event => setChoice(event.target.value)}
+            >
+              <FormControlLabel value="url" control={<Radio />} label="URL" />
+              <FormControlLabel value="file" control={<Radio />} label="File" />
+            </RadioGroup>
+          </FormControl>
+          {choice === 'url' ? (
+            <div>
+              <Typography>Open a InterProScan JSON file remote URL</Typography>
+              <TextField
+                label="URL"
+                value={interProURL}
+                onChange={event => setInterProURL(event.target.value)}
+              />
+            </div>
+          ) : null}
+          {choice === 'file' ? (
+            <div style={{ paddingTop: 20 }}>
+              <Typography>
+                Open a InterProScan JSON file file from your local drive
+              </Typography>
+              <Button variant="outlined" component="label">
+                Choose File
+                <input
+                  type="file"
+                  hidden
+                  onChange={({ target }) => {
+                    const file = target?.files?.[0]
+                    if (file) {
+                      setFile(file)
+                    }
+                  }}
+                />
+              </Button>
+            </div>
+          ) : null}
+        </div>
+      </DialogContent>
+      <DialogActions>
+        <Button
+          variant="contained"
+          color="primary"
+          onClick={() => {
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            ;(async () => {
+              try {
+                const ret: InterProScanResponse = file
+                  ? JSON.parse(await file.text())
+                  : await jsonfetch(interProURL)
+
+                model.setLoadedInterProAnnotations(
+                  Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])),
+                )
+                model.setShowDomains(true)
+                getSession(model).notify(
+                  'Loaded interproscan results',
+                  'success',
+                )
+              } catch (e) {
+                console.error(e)
+                getSession(model).notifyError(`${e}`, e)
+              } finally {
+                model.setStatus()
+              }
+            })()
+            handleClose()
+          }}
+        >
+          Open results
+        </Button>
+      </DialogActions>
+    </>
+  )
+})
+
+export default FeatureTypeDialog

package/src/components/header/Header.tsx

@@ -13,7 +13,6 @@ import ZoomControls from './ZoomControls'
 import MultiAlignmentSelector from './MultiAlignmentSelector'
 import HeaderInfoArea from './HeaderInfoArea'
 import HeaderStatusArea from './HeaderStatusArea'
-import HeaderMenu from './HeaderMenu'
 import HeaderMenuExtra from './HeaderMenuExtra'
 
 const AboutDialog = lazy(() => import('../dialogs/AboutDialog'))
@@ -21,7 +20,6 @@ const AboutDialog = lazy(() => import('../dialogs/AboutDialog'))
 const Header = observer(function ({ model }: { model: MsaViewModel }) {
   return (
     <div style={{ display: 'flex' }}>
-      <HeaderMenu model={model} />
       <ZoomControls model={model} />
       <HeaderMenuExtra model={model} />
       <MultiAlignmentSelector model={model} />

package/src/components/header/HeaderMenuExtra.tsx

@@ -3,7 +3,6 @@ import { observer } from 'mobx-react'
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'
 
 // locals
-import { MsaViewModel } from '../../model'
 
 // icons
 import MoreVert from '@mui/icons-material/MoreVert'
@@ -13,18 +12,50 @@ import FilterAlt from '@mui/icons-material/FilterAlt'
 import Search from '@mui/icons-material/Search'
 import PhotoCamera from '@mui/icons-material/PhotoCamera'
 import RestartAlt from '@mui/icons-material/RestartAlt'
+import FolderOpen from '@mui/icons-material/FolderOpen'
+import Settings from '@mui/icons-material/Settings'
+import Assignment from '@mui/icons-material/Assignment'
+import List from '@mui/icons-material/List'
+
+// locals
+import { 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 InterProScanDialog = lazy(() => import('../dialogs/InterProScanDialog'))
+const DomainDialog = lazy(() => import('../dialogs/DomainDialog'))
 
 const HeaderMenuExtra = observer(function ({ model }: { model: MsaViewModel }) {
-  const { featureMode, subFeatureRows, noAnnotations, interProScanJobIds } =
-    model
+  const { showDomains, subFeatureRows, noAnnotations } = model
   return (
     <CascadingMenuButton
       menuItems={[
+        {
+          label: 'Return to import form',
+          icon: FolderOpen,
+          onClick: () => model.reset(),
+        },
+        {
+          label: 'Settings',
+          onClick: () =>
+            model.queueDialog(onClose => [SettingsDialog, { model, onClose }]),
+          icon: Settings,
+        },
+        {
+          label: 'Metadata',
+          onClick: () =>
+            model.queueDialog(onClose => [MetadataDialog, { model, onClose }]),
+          icon: Assignment,
+        },
+        {
+          label: 'Extra tracks',
+          onClick: () =>
+            model.queueDialog(onClose => [TracklistDialog, { model, onClose }]),
+          icon: List,
+        },
         {
           label: 'Reset zoom to default',
           icon: RestartAlt,
@@ -47,9 +78,9 @@ const HeaderMenuExtra = observer(function ({ model }: { model: MsaViewModel }) {
               label:
                 'Show domains' + (noAnnotations ? ' (no domains loaded)' : ''),
               icon: Visibility,
-              checked: featureMode,
+              checked: showDomains,
               type: 'checkbox',
-              onClick: () => model.setFeatureMode(!featureMode),
+              onClick: () => model.setShowDomains(!showDomains),
             },
             {
               label: 'Use sub-row layout',
@@ -69,32 +100,14 @@ const HeaderMenuExtra = observer(function ({ model }: { model: MsaViewModel }) {
               },
             },
             {
-              label: 'Query InterProScan for domains...',
+              label: 'View domains',
               icon: Search,
               onClick: () =>
-                model.queueDialog(onClose => [
-                  InterProScanDialog,
-                  { onClose, model },
+                model.queueDialog(handleClose => [
+                  DomainDialog,
+                  { handleClose, model },
                 ]),
             },
-            {
-              label: 'Load previous InterProScan results...',
-              icon: Search,
-              type: 'subMenu',
-              subMenu: interProScanJobIds.length
-                ? interProScanJobIds.map(({ jobId, date }) => ({
-                    label:
-                      new Date(date).toLocaleString('en-US') + ' - ' + jobId,
-                    onClick: () => model.loadInterProScanResults(jobId),
-                  }))
-                : [
-                    {
-                      label: 'No previous searches',
-                      disabled: true,
-                      onClick: () => {},
-                    },
-                  ],
-            },
           ],
         },
         ...(model.extraViewMenuItems?.() || []),

package/src/components/header/HeaderStatusArea.tsx

@@ -2,6 +2,7 @@ import React from 'react'
 import { Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
+import { LoadingEllipses } from '@jbrowse/core/ui'
 
 // locals
 import { MsaViewModel } from '../../model'
@@ -13,12 +14,16 @@ const useStyles = makeStyles()({
   },
 })
 
-const HeaderStatusArea = observer(({ model }: { model: MsaViewModel }) => {
+const HeaderStatusArea = observer(function ({
+  model,
+}: {
+  model: MsaViewModel
+}) {
   const { status } = model
   const { classes } = useStyles()
   return status ? (
     <Typography className={classes.margin}>
-      {status.msg}{' '}
+      <LoadingEllipses message={status.msg} component="span" />{' '}
       {status.url ? (
         <a href={status.url} target="_blank" rel="noreferrer">
           (status)

package/src/components/msa/MSACanvas.tsx

@@ -1,6 +1,5 @@
 import React, { useEffect, useState, useRef } from 'react'
 import { observer } from 'mobx-react'
-import normalizeWheel from 'normalize-wheel'
 
 // locals
 import { MsaViewModel } from '../../model'
@@ -23,10 +22,9 @@ const MSACanvas = observer(function ({ model }: { model: MsaViewModel }) {
     if (!curr) {
       return
     }
-    function onWheel(origEvent: WheelEvent) {
-      const event = normalizeWheel(origEvent)
-      deltaX.current += event.pixelX
-      deltaY.current += event.pixelY
+    function onWheel(event: WheelEvent) {
+      deltaX.current += event.deltaX
+      deltaY.current += event.deltaY
 
       if (!scheduled.current) {
         scheduled.current = true
@@ -38,8 +36,8 @@ const MSACanvas = observer(function ({ model }: { model: MsaViewModel }) {
           scheduled.current = false
         })
       }
-      origEvent.preventDefault()
-      origEvent.stopPropagation()
+      event.preventDefault()
+      event.stopPropagation()
     }
     curr.addEventListener('wheel', onWheel)
     return () => {
@@ -121,9 +119,7 @@ const MSACanvas = observer(function ({ model }: { model: MsaViewModel }) {
         overflow: 'hidden',
       }}
     >
-      {!MSA && !msaFilehandle ? null : !MSA ? (
-        <Loading />
-      ) : (
+      {!MSA && !msaFilehandle ? null : MSA ? (
         blocks2d.map(([bx, by]) => (
           <MSACanvasBlock
             key={`${bx}_${by}`}
@@ -132,6 +128,8 @@ const MSACanvas = observer(function ({ model }: { model: MsaViewModel }) {
             offsetY={by}
           />
         ))
+      ) : (
+        <Loading />
       )}
     </div>
   )

package/src/components/msa/MSACanvasBlock.tsx

@@ -45,7 +45,7 @@ const MSABlock = observer(function ({
     return autorun(() => {
       ctx.resetTransform()
       ctx.clearRect(0, 0, blockSize, blockSize)
-      if (model.featureMode) {
+      if (model.showDomains) {
         renderBoxFeatureCanvasBlock({
           ctx,
           offsetX,