jbrowse-plugin-msaview 2.0.5 → 2.1.0

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/calculateProteinSequence.ts

@@ -1,15 +1,11 @@
 import {
-  Feature,
   defaultCodonTable,
   generateCodonTable,
   revcom,
 } from '@jbrowse/core/util'
 
-export interface Feat {
-  start: number
-  end: number
-  type: string
-}
+import type { Feat } from './types'
+import type { Feature } from '@jbrowse/core/util'
 
 export function stitch(subfeats: Feat[], sequence: string) {
   return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('')
@@ -33,10 +29,7 @@ export function calculateProteinSequence({
   return protein
 }
 
-export function revlist(
-  list: { start: number; end: number; type: string }[],
-  seqlen: number,
-) {
+export function revlist(list: Feat[], seqlen: number) {
   return list
     .map(sub => ({
       ...sub,
@@ -65,23 +58,16 @@ export function getProteinSequence({
   seq: string
   selectedTranscript: Feature
 }) {
-  // @ts-expect-error
-  const f = selectedTranscript.toJSON() as {
-    start: number
-    end: number
-    strand: number
-    type: string
-    subfeatures: { start: number; end: number; type: string }[]
-  }
+  const f = selectedTranscript.toJSON()
   const cds = dedupe(
     f.subfeatures
-      .sort((a, b) => a.start - b.start)
+      ?.sort((a, b) => a.start - b.start)
       .map(sub => ({
         ...sub,
         start: sub.start - f.start,
         end: sub.end - f.start,
       }))
-      .filter(f => f.type === 'CDS'),
+      .filter(f => f.type === 'CDS') || [],
   )
 
   return calculateProteinSequence({

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

@@ -0,0 +1,37 @@
+import { getConf } from '@jbrowse/core/configuration'
+
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util'
+
+export async function fetchSeq({
+  start,
+  end,
+  refName,
+  session,
+  assemblyName,
+}: {
+  start: number
+  end: number
+  refName: string
+  assemblyName: string
+  session: AbstractSessionModel
+}) {
+  const { assemblyManager, rpcManager } = session
+  const assembly = await assemblyManager.waitForAssembly(assemblyName)
+  if (!assembly) {
+    throw new Error('assembly not found')
+  }
+  const sessionId = 'getSequence'
+  const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+    adapterConfig: getConf(assembly, ['sequence', 'adapter']),
+    sessionId,
+    regions: [
+      {
+        start,
+        end,
+        refName: assembly.getCanonicalRefName(refName),
+        assemblyName,
+      },
+    ],
+  })) as Feature[]
+  return (feats[0]?.get('seq') as string | undefined) ?? ''
+}

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/NewNCBIBlastQuery/types.ts

@@ -0,0 +1,11 @@
+export interface Feat {
+  start: number
+  end: number
+  type?: string
+}
+
+export interface SeqState {
+  seq: string
+  upstream?: string
+  downstream?: string
+}

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

@@ -1,53 +1,17 @@
 import { useEffect, useState } from 'react'
 
-import { getConf } from '@jbrowse/core/configuration'
-import { AbstractSessionModel, Feature, getSession } from '@jbrowse/core/util'
+import { getSession } from '@jbrowse/core/util'
 
-export interface SeqState {
-  seq: string
-  upstream?: string
-  downstream?: string
-}
+import { fetchSeq } from './fetchSeq'
+
+import type { Feature } from '@jbrowse/core/util'
+import type { SeqState } from './types'
 
 export interface ErrorState {
   error: string
 }
 const BPLIMIT = 500_000
 
-async function fetchSeq({
-  start,
-  end,
-  refName,
-  session,
-  assemblyName,
-}: {
-  start: number
-  end: number
-  refName: string
-  assemblyName: string
-  session: AbstractSessionModel
-}) {
-  const { assemblyManager, rpcManager } = session
-  const assembly = await assemblyManager.waitForAssembly(assemblyName)
-  if (!assembly) {
-    throw new Error('assembly not found')
-  }
-  const sessionId = 'getSequence'
-  const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
-    adapterConfig: getConf(assembly, ['sequence', 'adapter']),
-    sessionId,
-    regions: [
-      {
-        start,
-        end,
-        refName: assembly.getCanonicalRefName(refName),
-        assemblyName,
-      },
-    ],
-  })) as Feature[]
-  return (feats[0]?.get('seq') as string | undefined) ?? ''
-}
-
 export function useFeatureSequence({
   view,
   feature,

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',
@@ -83,30 +83,24 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({
         </Typography>
         {error ? <ErrorMessage error={error} /> : null}
         {geneNameList && !ret ? (
-          <div style={{ color: 'red' }}>No MSA data for this gene found</div>
+          <Typography color="error">No MSA data for this gene found</Typography>
         ) : null}
         <TextField
+          select
+          label="Choose isoform to view MSA for"
           value={userSelection}
           onChange={event => {
             setUserSelection(event.target.value)
           }}
-          label="Choose isoform to view MSA for"
-          select
         >
-          {options
-            .filter(val => set.has(getId(val)))
-            .map(val => (
-              <MenuItem value={getId(val)} key={val.id()}>
-                {getTranscriptDisplayName(val)} (has data)
-              </MenuItem>
-            ))}
-          {options
-            .filter(val => !set.has(getId(val)))
-            .map(val => (
-              <MenuItem value={getId(val)} key={val.id()} disabled>
-                {getTranscriptDisplayName(val)}
+          {options.map(val => {
+            const inSet = set.has(getId(val))
+            return (
+              <MenuItem value={getId(val)} key={val.id()} disabled={!inSet}>
+                {getTranscriptDisplayName(val)} {inSet ? ' (has data)' : ''}
               </MenuItem>
-            ))}
+            )
+          })}
         </TextField>
       </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/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/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'

package/dist/LaunchMsaView/components/TabUtils.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-interface TabPanelProps {
-    children?: React.ReactNode;
-    index: number;
-    value: number;
-}
-export default function CustomTabPanel(props: TabPanelProps): React.JSX.Element;
-export {};

package/dist/LaunchMsaView/components/TabUtils.js

@@ -1,7 +0,0 @@
-import React from 'react';
-import { Box } from '@mui/material';
-export default function CustomTabPanel(props) {
-    const { children, value, index, ...other } = props;
-    return (React.createElement("div", { role: "tabpanel", hidden: value !== index, id: `gtabpanel-${index}`, "aria-labelledby": `gtab-${index}`, ...other }, value === index && React.createElement(Box, { sx: { p: 3 } }, children)));
-}
-//# sourceMappingURL=TabUtils.js.map

package/dist/LaunchMsaView/components/TabUtils.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"TabUtils.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabUtils.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,GAAG,EAAE,MAAM,eAAe,CAAA;AAQnC,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,KAAoB;IACzD,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,KAAK,EAAE,GAAG,KAAK,CAAA;IAElD,OAAO,CACL,6BACE,IAAI,EAAC,UAAU,EACf,MAAM,EAAE,KAAK,KAAK,KAAK,EACvB,EAAE,EAAE,aAAa,KAAK,EAAE,qBACP,QAAQ,KAAK,EAAE,KAC5B,KAAK,IAER,KAAK,KAAK,KAAK,IAAI,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,IAAG,QAAQ,CAAO,CACnD,CACP,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/tabUtil.d.ts

@@ -1,4 +0,0 @@
-export declare function a11yProps(index: number): {
-    id: string;
-    'aria-controls': string;
-};

package/dist/LaunchMsaView/components/tabUtil.js

@@ -1,7 +0,0 @@
-export function a11yProps(index) {
-    return {
-        id: `gtab-${index}`,
-        'aria-controls': `gtabpanel-${index}`,
-    };
-}
-//# sourceMappingURL=tabUtil.js.map

package/dist/LaunchMsaView/components/tabUtil.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"tabUtil.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/tabUtil.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,SAAS,CAAC,KAAa;IACrC,OAAO;QACL,EAAE,EAAE,QAAQ,KAAK,EAAE;QACnB,eAAe,EAAE,aAAa,KAAK,EAAE;KACtC,CAAA;AACH,CAAC"}

package/src/LaunchMsaView/components/TabUtils.tsx

@@ -1,25 +0,0 @@
-import React from 'react'
-
-import { Box } from '@mui/material'
-
-interface TabPanelProps {
-  children?: React.ReactNode
-  index: number
-  value: number
-}
-
-export default function CustomTabPanel(props: TabPanelProps) {
-  const { children, value, index, ...other } = props
-
-  return (
-    <div
-      role="tabpanel"
-      hidden={value !== index}
-      id={`gtabpanel-${index}`}
-      aria-labelledby={`gtab-${index}`}
-      {...other}
-    >
-      {value === index && <Box sx={{ p: 3 }}>{children}</Box>}
-    </div>
-  )
-}

package/src/LaunchMsaView/components/tabUtil.ts

@@ -1,6 +0,0 @@
-export function a11yProps(index: number) {
-  return {
-    id: `gtab-${index}`,
-    'aria-controls': `gtabpanel-${index}`,
-  }
-}