jbrowse-plugin-msaview 2.0.4 → 2.0.6

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.0.4",
+  "version": "2.0.6",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "keywords": [
@@ -24,9 +24,9 @@
   },
   "scripts": {
     "clean": "rimraf dist",
-    "start": "node esbuild.mjs",
+    "start": "node esbuild-watch.mjs",
     "format": "prettier --write .",
-    "build": "tsc && NODE_ENV=production node esbuild.mjs",
+    "build": "tsc && NODE_ENV=production node esbuild.mjs && cp distconfig.json dist/config.json",
     "prebuild": "npm run clean",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "prepack": "npm run build",
@@ -36,37 +36,39 @@
     "name": "MsaView"
   },
   "dependencies": {
+    "@emotion/styled": "^11.14.0",
     "g2p_mapper": "^1.0.4",
     "pako": "^2.1.0",
-    "react-msaview": "^3.0.3"
+    "react-msaview": "^4.0.0"
   },
   "devDependencies": {
     "@emotion/react": "^11.10.4",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
-    "@jbrowse/core": "^2.10.1",
-    "@jbrowse/plugin-linear-genome-view": "^2.7.0",
-    "@mui/icons-material": "^5.15.6",
-    "@mui/material": "^5.14.12",
-    "@mui/system": "^5.14.12",
-    "@mui/x-data-grid": "^7.13.0",
-    "@types/node": "^20.8.6",
+    "@jbrowse/core": "^3.0.1",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.1",
+    "@mui/icons-material": "^7.1.0",
+    "@mui/material": "^7.1.0",
+    "@mui/system": "^7.1.0",
+    "@mui/x-data-grid": "^8.2.0",
+    "@types/node": "^22.10.7",
     "@types/pako": "^2.0.1",
-    "@types/react": "^18.2.28",
+    "@types/react": "^19.0.7",
     "@typescript-eslint/eslint-plugin": "^8.0.1",
     "@typescript-eslint/parser": "^8.0.1",
-    "esbuild": "^0.23.0",
+    "esbuild": "^0.25.4",
     "eslint": "^9.0.0",
+    "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-react": "^7.20.3",
-    "eslint-plugin-react-hooks": "next",
+    "eslint-plugin-react-hooks": "^5.0.0",
     "eslint-plugin-react-refresh": "^0.4.9",
-    "eslint-plugin-unicorn": "^55.0.0",
+    "eslint-plugin-unicorn": "^59.0.1",
     "mobx": "^6.10.2",
     "mobx-react": "^9.0.1",
     "mobx-state-tree": "^5.3.0",
     "prettier": "^3.0.3",
-    "pretty-bytes": "^6.1.1",
-    "react": "^18.2.0",
-    "react-dom": "^18.2.0",
+    "pretty-bytes": "^7.0.0",
+    "react": "^19.0.0",
+    "react-dom": "^19.0.0",
     "rimraf": "^6.0.0",
     "rxjs": "^7.8.1",
     "tss-react": "^4.9.2",

package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx

@@ -1,9 +1,12 @@
 import React from 'react'
-import { observer } from 'mobx-react'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
 import { getSession } from '@jbrowse/core/util'
+import { observer } from 'mobx-react'
+
 import { useStyles } from './util'
 
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
 const GenomeMouseoverHighlight = observer(function GenomeMouseoverHighlight2({
   model,
 }: {

package/src/AddHighlightModel/HighlightComponents.tsx

@@ -1,10 +1,11 @@
 import React from 'react'
+
 import { observer } from 'mobx-react'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
-// locals
-import MsaToGenomeHighlight from './MsaToGenomeHighlight'
 import GenomeMouseoverHighlight from './GenomeMouseoverHighlight'
+import MsaToGenomeHighlight from './MsaToGenomeHighlight'
+
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 type LGV = LinearGenomeViewModel
 

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -1,13 +1,13 @@
 import React from 'react'
-import { observer } from 'mobx-react'
-import { getSession } from '@jbrowse/core/util'
 
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { getSession } from '@jbrowse/core/util'
+import { observer } from 'mobx-react'
 
-// locals
-import { JBrowsePluginMsaViewModel } from '../MsaViewPanel/model'
 import { useStyles } from './util'
+import { JBrowsePluginMsaViewModel } from '../MsaViewPanel/model'
+
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 type LGV = LinearGenomeViewModel
 

package/src/AddHighlightModel/index.tsx

@@ -1,10 +1,11 @@
 import React from 'react'
+
 import PluginManager from '@jbrowse/core/PluginManager'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
-// locals
 import HighlightComponents from './HighlightComponents'
 
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
 export default function AddHighlightComponentsModelF(
   pluginManager: PluginManager,
 ) {

package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx

@@ -1,13 +1,12 @@
 import React, { useState } from 'react'
+
 import { Dialog } from '@jbrowse/core/ui'
-import { Box, Tab, Tabs } from '@mui/material'
 import { AbstractTrackModel, Feature } from '@jbrowse/core/util'
+import { Box, Tab, Tabs } from '@mui/material'
 
-// locals
-
-import CustomTabPanel from './TabUtils'
 import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery'
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel'
+import CustomTabPanel from './TabUtils'
 import { a11yProps } from './tabUtil'
 
 export default function LaunchProteinViewDialog({

package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx

@@ -1,26 +1,27 @@
 import React, { useState } from 'react'
-import { observer } from 'mobx-react'
-import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
+
+import { ErrorMessage } from '@jbrowse/core/ui'
 import {
   AbstractTrackModel,
   Feature,
   getContainingView,
 } from '@jbrowse/core/util'
-import { ErrorMessage } from '@jbrowse/core/ui'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material'
+import { observer } from 'mobx-react'
+import { makeStyles } from 'tss-react/mui'
 
-// locals
+import { getProteinSequence } from './calculateProteinSequence'
+import { ncbiBlastLaunchView } from './ncbiBlastLaunchView'
+import { useFeatureSequence } from './useFeatureSequence'
+import TextField2 from '../../../TextField2'
 import {
+  getGeneDisplayName,
   getId,
   getTranscriptDisplayName,
   getTranscriptFeatures,
-  getGeneDisplayName,
 } from '../../util'
-import { getProteinSequence } from './calculateProteinSequence'
-import { useFeatureSequence } from './useFeatureSequence'
-import TextField2 from '../../../TextField2'
-import { ncbiBlastLaunchView } from './ncbiBlastLaunchView'
+
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 const useStyles = makeStyles()({
   dialogContent: {
@@ -120,10 +121,12 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({
             ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
             : 'Loading...'
         }
-        InputProps={{
-          readOnly: true,
-          classes: {
-            input: classes.textAreaFont,
+        slotProps={{
+          input: {
+            readOnly: true,
+            classes: {
+              input: classes.textAreaFont,
+            },
           },
         }}
       />

package/src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts

@@ -1,7 +1,7 @@
 import { Feature, getSession } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-// locals
-import { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model'
+
+import type { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 export function ncbiBlastLaunchView({
   newViewTitle,

package/src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts

@@ -1,7 +1,7 @@
 import { useEffect, useState } from 'react'
 
-import { AbstractSessionModel, Feature, getSession } from '@jbrowse/core/util'
 import { getConf } from '@jbrowse/core/configuration'
+import { AbstractSessionModel, Feature, getSession } from '@jbrowse/core/util'
 
 export interface SeqState {
   seq: string

package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx

@@ -1,6 +1,12 @@
 import React, { useEffect, useState } from 'react'
-import { observer } from 'mobx-react'
+
 import { ErrorMessage } from '@jbrowse/core/ui'
+import {
+  AbstractTrackModel,
+  Feature,
+  getContainingView,
+  getSession,
+} from '@jbrowse/core/util'
 import {
   Button,
   DialogActions,
@@ -9,24 +15,19 @@ import {
   TextField,
   Typography,
 } from '@mui/material'
-import {
-  AbstractTrackModel,
-  Feature,
-  getContainingView,
-  getSession,
-} from '@jbrowse/core/util'
+import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
-// locals
+import { fetchGeneList } from './fetchGeneList'
+import { preCalculatedLaunchView } from './preCalculatedLaunchView'
 import {
-  getTranscriptDisplayName,
+  getGeneDisplayName,
   getId,
+  getTranscriptDisplayName,
   getTranscriptFeatures,
-  getGeneDisplayName,
 } from '../../util'
-import { fetchGeneList } from './fetchGeneList'
-import { preCalculatedLaunchView } from './preCalculatedLaunchView'
+
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 const useStyles = makeStyles()({
   dialogContent: {

package/src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts

@@ -1,7 +1,8 @@
 import { AbstractSessionModel, Feature } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { ungzip } from 'pako'
 
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
 async function myfetch(url: string) {
   const res = await fetch(url)
   if (!res.ok) {

package/src/LaunchMsaView/components/TabUtils.tsx

@@ -1,4 +1,5 @@
 import React from 'react'
+
 import { Box } from '@mui/material'
 
 interface TabPanelProps {

package/src/LaunchMsaView/index.ts

@@ -1,15 +1,13 @@
 import PluginManager from '@jbrowse/core/PluginManager'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
 import { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
-import { IAnyModelType } from 'mobx-state-tree'
-import { getSession, getContainingTrack, Feature } from '@jbrowse/core/util'
-
-// icons
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
+import { MenuItem } from '@jbrowse/core/ui'
+import { Feature, getContainingTrack, getSession } from '@jbrowse/core/util'
 import AddIcon from '@mui/icons-material/Add'
 
-// locals
 import LaunchMsaViewDialog from './components/LaunchMsaViewDialog'
-import { MenuItem } from '@jbrowse/core/ui'
+
+import type { IAnyModelType } from 'mobx-state-tree'
 
 function isDisplay(elt: { name: string }): elt is DisplayType {
   return elt.name === 'LinearBasicDisplay'

package/src/LaunchMsaView/util.ts

@@ -12,7 +12,7 @@ export function getTranscriptFeatures(feature: Feature) {
       )
 }
 export function getId(val?: Feature): string {
-  return val?.get('name') || val?.get('id') || ''
+  return val?.get('name') ?? val?.get('id') ?? ''
 }
 
 export function getTranscriptDisplayName(val?: Feature) {
@@ -24,7 +24,7 @@ export function getTranscriptDisplayName(val?: Feature) {
 export function getGeneDisplayName(val?: Feature) {
   return val === undefined
     ? ''
-    : [val.get('gene_name') || val.get('name'), val.get('id')]
+    : [val.get('gene_name') ?? val.get('name'), val.get('id')]
         .filter(f => !!f)
         .join(' ')
 }

package/src/MsaViewPanel/components/LoadingBLAST.tsx

@@ -1,11 +1,11 @@
 import React from 'react'
-import { JBrowsePluginMsaViewModel } from '../model'
+
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
 import { Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
-import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
 
-// locals
+import { JBrowsePluginMsaViewModel } from '../model'
 import RIDLink from './RIDLink'
 
 const useStyles = makeStyles()(theme => ({

package/src/MsaViewPanel/components/MsaViewPanel.tsx

@@ -1,8 +1,8 @@
 import React from 'react'
+
 import { observer } from 'mobx-react'
 import { MSAView } from 'react-msaview'
 
-// locals
 import { JBrowsePluginMsaViewModel } from '../model'
 import LoadingBLAST from './LoadingBLAST'
 

package/src/MsaViewPanel/components/RIDLink.tsx

@@ -1,6 +1,7 @@
 import React from 'react'
+
 import { Link, Typography } from '@mui/material'
-// locals
+
 import OpenInNewIcon from '../../OpenInNewIcon'
 import { BLAST_URL } from '../../utils/ncbiBlast'
 

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -1,10 +1,10 @@
-import { launchMSA } from '../utils/msa'
-import { queryBlast } from '../utils/ncbiBlast'
+import { JBrowsePluginMsaViewModel } from './model'
 import {
   makeId,
   strip,
 } from '../LaunchMsaView/components/NewNCBIBlastQuery/util'
-import { JBrowsePluginMsaViewModel } from './model'
+import { launchMSA } from '../utils/msa'
+import { queryBlast } from '../utils/ncbiBlast'
 
 export async function doLaunchBlast({
   self,

package/src/MsaViewPanel/genomeToMSA.ts

@@ -1,6 +1,7 @@
 import { getSession } from '@jbrowse/core/util'
-import { checkHovered } from './util'
+
 import { JBrowsePluginMsaViewModel } from './model'
+import { checkHovered } from './util'
 
 export function genomeToMSA({ model }: { model: JBrowsePluginMsaViewModel }) {
   const { hovered } = getSession(model)

package/src/MsaViewPanel/index.ts

@@ -1,8 +1,8 @@
 import { lazy } from 'react'
+
 import PluginManager from '@jbrowse/core/PluginManager'
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 
-// locals
 import stateModelFactory from './model'
 
 // lazies

package/src/MsaViewPanel/model.ts

@@ -1,15 +1,17 @@
-import { Instance, addDisposer, cast, types } from 'mobx-state-tree'
+import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
+import { getSession } from '@jbrowse/core/util'
+import { genomeToTranscriptSeqMapping } from 'g2p_mapper'
 import { autorun } from 'mobx'
+import { addDisposer, cast, types } from 'mobx-state-tree'
 import { MSAModelF } from 'react-msaview'
-import { Feature, getSession } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
 
-// locals
 import { doLaunchBlast } from './doLaunchBlast'
 import { genomeToMSA } from './genomeToMSA'
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
-import { genomeToTranscriptSeqMapping } from 'g2p_mapper'
+
+import type { Feature } from '@jbrowse/core/util'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { Instance } from 'mobx-state-tree'
 
 type LGV = LinearGenomeViewModel
 
@@ -71,8 +73,17 @@ export default function stateModelFactory() {
     )
 
     .volatile(() => ({
+      /**
+       * #volatile
+       */
       rid: undefined as string | undefined,
+      /**
+       * #volatile
+       */
       progress: '',
+      /**
+       * #volatile
+       */
       error: undefined as unknown,
     }))
 

package/src/MsaViewPanel/msaCoordToGenomeCoord.ts

@@ -1,4 +1,3 @@
-// locals
 import { JBrowsePluginMsaViewModel } from './model'
 
 export function msaCoordToGenomeCoord({

package/src/OpenInNewIcon.tsx

@@ -1,5 +1,8 @@
 import React from 'react'
-import { SvgIcon, SvgIconProps } from '@mui/material'
+
+import { SvgIcon } from '@mui/material'
+
+import type { SvgIconProps } from '@mui/material'
 
 export default function OpenInNewIcon(props: SvgIconProps) {
   return (

package/src/TextField2.tsx

@@ -1,5 +1,8 @@
 import React from 'react'
-import { TextField, TextFieldProps } from '@mui/material'
+
+import { TextField } from '@mui/material'
+
+import type { TextFieldProps } from '@mui/material'
 
 function TextField2({ children, ...rest }: TextFieldProps) {
   return (

package/src/index.ts

@@ -1,15 +1,12 @@
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
-
-// icons
 import GridOn from '@mui/icons-material/GridOn'
 
-// locals
 import { version } from '../package.json'
-import MsaViewF from './MsaViewPanel'
-import LaunchMsaViewF from './LaunchMsaView'
 import AddHighlightModelF from './AddHighlightModel'
+import LaunchMsaViewF from './LaunchMsaView'
+import MsaViewF from './MsaViewPanel'
 
 export default class MsaViewPlugin extends Plugin {
   name = 'MsaViewPlugin'