jbrowse-plugin-msaview 2.0.5 → 2.0.6

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.0.5",
+  "version": "2.0.6",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "keywords": [
@@ -26,7 +26,7 @@
     "clean": "rimraf dist",
     "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",

package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx

@@ -1,11 +1,12 @@
 import React from 'react'
 
 import { getSession } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 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

@@ -1,12 +1,12 @@
 import React from 'react'
 
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { observer } from 'mobx-react'
 
-// locals
 import GenomeMouseoverHighlight from './GenomeMouseoverHighlight'
 import MsaToGenomeHighlight from './MsaToGenomeHighlight'
 
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
 type LGV = LinearGenomeViewModel
 
 const HighlightComponents = observer(function HighlightComponents2({

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -2,14 +2,13 @@ import React from 'react'
 
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getSession } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { observer } from 'mobx-react'
 
-
-// locals
 import { useStyles } from './util'
 import { JBrowsePluginMsaViewModel } from '../MsaViewPanel/model'
 
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
 type LGV = LinearGenomeViewModel
 
 function getCanonicalName(assembly: Assembly, s: string) {

package/src/AddHighlightModel/index.tsx

@@ -1,11 +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

@@ -4,8 +4,6 @@ import { Dialog } from '@jbrowse/core/ui'
 import { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 import { Box, Tab, Tabs } from '@mui/material'
 
-// locals
-
 import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery'
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel'
 import CustomTabPanel from './TabUtils'

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

@@ -6,12 +6,10 @@ import {
   Feature,
   getContainingView,
 } from '@jbrowse/core/util'
-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'
@@ -23,6 +21,8 @@ import {
   getTranscriptFeatures,
 } from '../../util'
 
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
 const useStyles = makeStyles()({
   dialogContent: {
     width: '80em',
@@ -121,10 +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

@@ -1,8 +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/PreLoadedMSA/PreLoadedMSADataPanel.tsx

@@ -7,7 +7,6 @@ import {
   getContainingView,
   getSession,
 } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import {
   Button,
   DialogActions,
@@ -19,7 +18,6 @@ import {
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-// locals
 import { fetchGeneList } from './fetchGeneList'
 import { preCalculatedLaunchView } from './preCalculatedLaunchView'
 import {
@@ -29,6 +27,8 @@ import {
   getTranscriptFeatures,
 } from '../../util'
 
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
 const useStyles = makeStyles()({
   dialogContent: {
     width: '80em',

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/index.ts

@@ -4,13 +4,10 @@ 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'
-import { IAnyModelType } from 'mobx-state-tree'
 
-// icons
-
-// locals
 import LaunchMsaViewDialog from './components/LaunchMsaViewDialog'
 
+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

@@ -6,8 +6,6 @@ import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
 import { JBrowsePluginMsaViewModel } from '../model'
-
-// locals
 import RIDLink from './RIDLink'
 
 const useStyles = makeStyles()(theme => ({

package/src/MsaViewPanel/components/MsaViewPanel.tsx

@@ -3,7 +3,6 @@ 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

@@ -2,7 +2,6 @@ import React from 'react'
 
 import { Link, Typography } from '@mui/material'
 
-// locals
 import OpenInNewIcon from '../../OpenInNewIcon'
 import { BLAST_URL } from '../../utils/ncbiBlast'
 

package/src/MsaViewPanel/index.ts

@@ -3,7 +3,6 @@ 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

@@ -1,16 +1,17 @@
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
-import { Feature, getSession } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { getSession } from '@jbrowse/core/util'
 import { genomeToTranscriptSeqMapping } from 'g2p_mapper'
 import { autorun } from 'mobx'
-import { Instance, addDisposer, cast, types } from 'mobx-state-tree'
+import { addDisposer, cast, types } from 'mobx-state-tree'
 import { MSAModelF } from 'react-msaview'
 
-// locals
 import { doLaunchBlast } from './doLaunchBlast'
 import { genomeToMSA } from './genomeToMSA'
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
 
+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
 
@@ -72,8 +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

@@ -1,6 +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

@@ -1,6 +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

@@ -1,11 +1,8 @@
 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 AddHighlightModelF from './AddHighlightModel'
 import LaunchMsaViewF from './LaunchMsaView'