jbrowse-plugin-msaview 2.0.6 → 2.1.0

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/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

@@ -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/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/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 @@
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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}`,
-  }
-}