jbrowse-plugin-msaview 2.0.6 → 2.2.0

package/src/MsaViewPanel/components/LoadingBLAST.tsx

@@ -17,20 +17,36 @@ const useStyles = makeStyles()(theme => ({
   },
 }))
 
-function RIDError({ rid, error }: { rid?: string; error: unknown }) {
+function RIDError({
+  baseUrl,
+  rid,
+  error,
+}: {
+  baseUrl: string
+  rid?: string
+  error: unknown
+}) {
   return (
     <div>
-      {rid ? <RIDLink rid={rid} /> : null}
+      {rid ? <RIDLink rid={rid} baseUrl={baseUrl} /> : null}
       <ErrorMessage error={error} />
     </div>
   )
 }
 
-function RIDProgress({ rid, progress }: { rid: string; progress: string }) {
+function RIDProgress({
+  baseUrl,
+  rid,
+  progress,
+}: {
+  baseUrl: string
+  rid: string
+  progress: string
+}) {
   const { classes } = useStyles()
   return (
     <div className={classes.loading}>
-      {rid ? <RIDLink rid={rid} /> : null}
+      {rid ? <RIDLink baseUrl={baseUrl} rid={rid} /> : null}
       <Typography>{progress}</Typography>
     </div>
   )
@@ -38,8 +54,10 @@ function RIDProgress({ rid, progress }: { rid: string; progress: string }) {
 
 const LoadingBLAST = observer(function LoadingBLAST2({
   model,
+  baseUrl,
 }: {
   model: JBrowsePluginMsaViewModel
+  baseUrl: string
 }) {
   const { progress, rid, error, processing } = model
   const { classes } = useStyles()
@@ -47,10 +65,10 @@ const LoadingBLAST = observer(function LoadingBLAST2({
     <div className={classes.margin}>
       <LoadingEllipses message="Running NCBI BLAST" variant="h5" />
       {error ? (
-        <RIDError rid={rid} error={error} />
-      ) : (rid ? (
-        <RIDProgress rid={rid} progress={progress} />
-      ) : null)}
+        <RIDError baseUrl={baseUrl} rid={rid} error={error} />
+      ) : rid ? (
+        <RIDProgress baseUrl={baseUrl} rid={rid} progress={progress} />
+      ) : null}
       <Typography>{processing || 'Initializing BLAST query'}</Typography>
     </div>
   )

package/src/MsaViewPanel/components/MsaViewPanel.tsx

@@ -14,7 +14,11 @@ const MsaViewPanel = observer(function MsaViewPanel2({
   const { blastParams } = model
   return (
     <div>
-      {blastParams ? <LoadingBLAST model={model} /> : <MSAView model={model} />}
+      {blastParams ? (
+        <LoadingBLAST model={model} baseUrl={blastParams.baseUrl} />
+      ) : (
+        <MSAView model={model} />
+      )}
     </div>
   )
 })

package/src/MsaViewPanel/components/RIDLink.tsx

@@ -1,17 +1,17 @@
 import React from 'react'
 
-import { Link, Typography } from '@mui/material'
+import { Typography } from '@mui/material'
 
-import OpenInNewIcon from '../../OpenInNewIcon'
-import { BLAST_URL } from '../../utils/ncbiBlast'
+import ExternalLink from '../../ExternalLink'
 
-function RIDLink({ rid }: { rid: string }) {
+function RIDLink({ baseUrl, rid }: { rid: string; baseUrl: string }) {
   return (
     <Typography>
-      RID {rid}{' '}
-      <Link target="_black" href={`${BLAST_URL}?CMD=Get&RID=${rid}`}>
-        (see status at NCBI <OpenInNewIcon />)
-      </Link>
+      RID {rid} (
+      <ExternalLink href={`${baseUrl}?CMD=Get&RID=${rid}`}>
+        see status
+      </ExternalLink>
+      )
     </Typography>
   )
 }

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -1,8 +1,5 @@
 import { JBrowsePluginMsaViewModel } from './model'
-import {
-  makeId,
-  strip,
-} from '../LaunchMsaView/components/NewNCBIBlastQuery/util'
+import { makeId, strip } from '../LaunchMsaView/components/util'
 import { launchMSA } from '../utils/msa'
 import { queryBlast } from '../utils/ncbiBlast'
 
@@ -11,13 +8,18 @@ export async function doLaunchBlast({
 }: {
   self: JBrowsePluginMsaViewModel
 }) {
-  const { blastDatabase, blastProgram, msaAlgorithm, proteinSequence } =
-    self.blastParams!
-  const query = proteinSequence.replaceAll('*', '').replaceAll('&', '')
+  const {
+    baseUrl,
+    blastDatabase,
+    blastProgram,
+    msaAlgorithm,
+    proteinSequence,
+  } = self.blastParams!
   const { hits } = await queryBlast({
-    query,
+    query: proteinSequence.replaceAll('*', '').replaceAll('&', ''),
     blastDatabase,
     blastProgram,
+    baseUrl,
     onProgress: arg => {
       self.setProgress(arg)
     },
@@ -26,31 +28,28 @@ export async function doLaunchBlast({
     },
   })
 
-  const sequence = [
-    `>QUERY\n${query}`,
-    ...hits
-      .map(
-        h =>
-          [
-            makeId(
-              h.description[0] ?? {
-                accession: 'unknown',
-                id: 'unknown',
-                sciname: 'unknown',
-              },
-            ),
-            strip(h.hsps[0]?.hseq ?? ''),
-          ] as const,
-      )
-      .map(([id, seq]) => `>${id}\n${seq}`),
-  ].join('\n')
-
-  const data = await launchMSA({
+  return launchMSA({
     algorithm: msaAlgorithm,
-    sequence,
+    sequence: [
+      `>QUERY\n${proteinSequence.replaceAll('*', '').replaceAll('&', '')}`,
+      ...hits
+        .map(
+          h =>
+            [
+              makeId(
+                h.description[0] ?? {
+                  accession: 'unknown',
+                  id: 'unknown',
+                  sciname: 'unknown',
+                },
+              ),
+              strip(h.hsps[0]?.hseq ?? ''),
+            ] as const,
+        )
+        .map(([id, seq]) => `>${id}\n${seq}`),
+    ].join('\n'),
     onProgress: arg => {
       self.setProgress(arg)
     },
   })
-  return data
 }

package/src/MsaViewPanel/model.ts

@@ -24,6 +24,7 @@ export interface IRegion {
 }
 
 export interface BlastParams {
+  baseUrl: string
   blastDatabase: string
   msaAlgorithm: string
   blastProgram: string

package/src/ReadOnlyTextField2.tsx

@@ -0,0 +1,33 @@
+import React from 'react'
+
+import { makeStyles } from 'tss-react/mui'
+
+import TextField2 from './TextField2'
+
+const useStyles = makeStyles()({
+  textAreaFont: {
+    fontFamily: 'Courier New',
+  },
+})
+
+export default function ReadOnlyTextField2({ value }: { value: string }) {
+  const { classes } = useStyles()
+  return (
+    <TextField2
+      variant="outlined"
+      multiline
+      minRows={5}
+      maxRows={10}
+      fullWidth
+      value={value}
+      slotProps={{
+        input: {
+          readOnly: true,
+          classes: {
+            input: classes.textAreaFont,
+          },
+        },
+      }}
+    />
+  )
+}

package/src/index.ts

@@ -1,7 +1,9 @@
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
 import GridOn from '@mui/icons-material/GridOn'
+import { types } from 'mobx-state-tree'
 
 import { version } from '../package.json'
 import AddHighlightModelF from './AddHighlightModel'
@@ -29,4 +31,25 @@ export default class MsaViewPlugin extends Plugin {
       })
     }
   }
+
+  rootConfigurationSchema = {
+    msa: ConfigurationSchema('MSA', {
+      datasets: types.maybe(
+        types.array(
+          ConfigurationSchema('MSAEntry', {
+            name: {
+              type: 'string',
+              defaultValue: '',
+            },
+            adapter: {
+              type: 'frozen',
+              description:
+                'This can be a data adapter config for a IndexedFasta for example, which has a special way of being interpreted',
+              defaultValue: {},
+            },
+          }),
+        ),
+      ),
+    }),
+  }
 }

package/src/utils/fetch.ts

@@ -15,9 +15,9 @@ export async function textfetch(url: string, args?: RequestInit) {
   return response.text()
 }
 
-export async function jsonfetch(url: string, args?: RequestInit) {
+export async function jsonfetch<T>(url: string, args?: RequestInit) {
   const response = await myfetch(url, args)
-  return response.json()
+  return response.json() as Promise<T>
 }
 
 export function timeout(time: number) {

package/src/utils/ncbiBlast.ts

@@ -1,17 +1,18 @@
 import { jsonfetch, textfetch, timeout } from './fetch'
-
-export const BLAST_URL = `https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi`
+import { BlastResults } from './types'
 
 export async function queryBlast({
   query,
   blastDatabase,
   blastProgram,
+  baseUrl,
   onProgress,
   onRid,
 }: {
   query: string
   blastDatabase: string
   blastProgram: string
+  baseUrl: string
   onProgress: (arg: string) => void
   onRid: (arg: string) => void
 }) {
@@ -20,25 +21,17 @@ export async function queryBlast({
     query,
     blastDatabase,
     blastProgram,
+    baseUrl,
   })
   onRid(rid)
-  await waitForRid({ rid, onProgress })
-  const ret = (await jsonfetch(
-    `${BLAST_URL}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
-  )) as {
-    BlastOutput2: {
-      report: {
-        results: {
-          search: {
-            hits: {
-              description: { accession: string; id: string; sciname: string }[]
-              hsps: { hseq: string }[]
-            }[]
-          }
-        }
-      }
-    }[]
-  }
+  await waitForRid({
+    rid,
+    onProgress,
+    baseUrl,
+  })
+  const ret = await jsonfetch<BlastResults>(
+    `${baseUrl}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
+  )
   return {
     rid,
     hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
@@ -49,16 +42,18 @@ async function initialQuery({
   query,
   blastProgram,
   blastDatabase,
+  baseUrl,
 }: {
   query: string
   blastProgram: string
   blastDatabase: string
+  baseUrl: string
 }) {
-  const res = await textfetch(BLAST_URL, {
+  const res = await textfetch(baseUrl, {
     method: 'POST',
     body: new URLSearchParams({
       CMD: 'Put',
-      PROGRAM: blastProgram,
+      PROGRAM: blastProgram === 'quick-blastp' ? 'blastp' : blastProgram,
       DATABASE: blastDatabase,
       QUERY: query,
       ...(blastDatabase === 'nr_clustered_seq'
@@ -67,6 +62,9 @@ async function initialQuery({
             DB_TYPE: 'Experimental Databases',
           }
         : {}),
+      ...(blastProgram === 'quick-blastp'
+        ? { BLAST_PROGRAMS: 'kmerBlastp' }
+        : {}),
     }),
   })
 
@@ -79,15 +77,20 @@ async function initialQuery({
   if (!rid) {
     throw new Error('Failed to get RID from BLAST request')
   }
-  return { rid, rtoe }
+  return {
+    rid,
+    rtoe,
+  }
 }
 
 async function waitForRid({
   rid,
   onProgress,
+  baseUrl,
 }: {
   rid: string
   onProgress: (arg: string) => void
+  baseUrl: string
 }) {
   // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
@@ -98,16 +101,23 @@ async function waitForRid({
     }
 
     const res = await textfetch(
-      `${BLAST_URL}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
+      `${baseUrl}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
     )
-    if (/\s+Status=WAITING/m.test(res)) {
+    const isWaiting = /\s+Status=WAITING/m.test(res)
+    const isFailed = /\s+Status=FAILED/m.test(res)
+    const isReady = /\s+Status=READY/m.test(res)
+    const hasHits = /\s+ThereAreHits=yes/m.test(res)
+
+    if (isWaiting) {
       continue
-    } else if (/\s+Status=FAILED/m.test(res)) {
-      throw new Error(
-        `BLAST ${rid} failed; please report to blast-help@ncbi.nlm.nih.gov`,
-      )
-    } else if (/\s+Status=READY/m.test(res)) {
-      if (/\s+ThereAreHits=yes/m.test(res)) {
+    }
+
+    if (isFailed) {
+      throw new Error(`BLAST ${rid} failed`)
+    }
+
+    if (isReady) {
+      if (hasHits) {
         return true
       } else {
         throw new Error('No hits found')

package/src/utils/types.ts

@@ -0,0 +1,14 @@
+export interface BlastResults {
+  BlastOutput2: {
+    report: {
+      results: {
+        search: {
+          hits: {
+            description: { accession: string; id: string; sciname: string }[]
+            hsps: { hseq: string }[]
+          }[]
+        }
+      }
+    }
+  }[]
+}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js

@@ -1,85 +0,0 @@
-import React, { useState } from 'react';
-import { ErrorMessage } from '@jbrowse/core/ui';
-import { getContainingView, } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { getProteinSequence } from './calculateProteinSequence';
-import { ncbiBlastLaunchView } from './ncbiBlastLaunchView';
-import { useFeatureSequence } from './useFeatureSequence';
-import TextField2 from '../../../TextField2';
-import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
-const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-    },
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-});
-const NcbiBlastPanel = observer(function NcbiBlastPanel2({ handleClose, feature, model, }) {
-    const { classes } = useStyles();
-    const view = getContainingView(model);
-    const [blastDatabase, setBlastDatabase] = useState('nr');
-    const [msaAlgorithm, setMsaAlgorithm] = useState('clustalo');
-    const options = getTranscriptFeatures(feature);
-    const [userSelection, setUserSelection] = useState(getId(options[0]));
-    const selectedTranscript = options.find(val => getId(val) === userSelection);
-    const { sequence, error } = useFeatureSequence({
-        view,
-        feature: selectedTranscript,
-    });
-    const proteinSequence = sequence && !('error' in sequence)
-        ? getProteinSequence({
-            seq: sequence.seq,
-            selectedTranscript,
-        })
-        : '';
-    const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
-    const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
-    return (React.createElement(DialogContent, { className: classes.dialogContent },
-        error ? React.createElement(ErrorMessage, { error: error }) : null,
-        React.createElement(TextField2, { value: blastDatabase, onChange: event => {
-                setBlastDatabase(event.target.value);
-            }, label: "BLAST blastDatabase", select: true }, blastDatabaseOptions.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-        React.createElement(TextField2, { value: msaAlgorithm, onChange: event => {
-                setMsaAlgorithm(event.target.value);
-            }, label: "MSA Algorithm", select: true }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-        React.createElement(TextField2, { value: userSelection, onChange: event => {
-                setUserSelection(event.target.value);
-            }, label: "Choose isoform to BLAST", select: true }, options.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
-            getGeneDisplayName(feature),
-            " - ",
-            getTranscriptDisplayName(val))))),
-        React.createElement(TextField2, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, value: proteinSequence
-                ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
-                : 'Loading...', slotProps: {
-                input: {
-                    readOnly: true,
-                    classes: {
-                        input: classes.textAreaFont,
-                    },
-                },
-            } }),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
-                    const newView = ncbiBlastLaunchView({
-                        feature: selectedTranscript,
-                        view,
-                        newViewTitle: `NCBI BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)} - ${msaAlgorithm}`,
-                    });
-                    newView.setBlastParams({
-                        blastProgram: 'blastp',
-                        blastDatabase,
-                        msaAlgorithm,
-                        selectedTranscript,
-                        proteinSequence,
-                    });
-                    handleClose();
-                }, disabled: !proteinSequence }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
-});
-export default NcbiBlastPanel;
-//# sourceMappingURL=NcbiBlastPanel.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"NcbiBlastPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAGL,iBAAiB,GAClB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAA;AAC/D,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAA;AAC3D,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAA;AACzD,OAAO,UAAU,MAAM,qBAAqB,CAAA;AAC5C,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,YAAY,CAAA;AAInB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,SAAS,eAAe,CAAC,EACvD,WAAW,EACX,OAAO,EACP,KAAK,GAKN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IACxD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;IAE5D,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAE,CAAA;IAC7E,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,kBAAkB,CAAC;QAC7C,IAAI;QACJ,OAAO,EAAE,kBAAkB;KAC5B,CAAC,CAAA;IACF,MAAM,eAAe,GACnB,QAAQ,IAAI,CAAC,CAAC,OAAO,IAAI,QAAQ,CAAC;QAChC,CAAC,CAAC,kBAAkB,CAAC;YACjB,GAAG,EAAE,QAAQ,CAAC,GAAG;YACjB,kBAAkB;SACnB,CAAC;QACJ,CAAC,CAAC,EAAE,CAAA;IAER,MAAM,oBAAoB,GAAG,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACrD,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAA;IAC/D,OAAO,CACL,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;QAC5C,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,oBAAC,UAAU,IACT,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACtC,CAAC,EACD,KAAK,EAAC,qBAAqB,EAC3B,MAAM,UAEL,oBAAoB,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAC/B,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;QAEb,oBAAC,UAAU,IACT,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACrC,CAAC,EACD,KAAK,EAAC,eAAe,EACrB,MAAM,UAEL,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;QAEb,oBAAC,UAAU,IACT,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACtC,CAAC,EACD,KAAK,EAAC,yBAAyB,EAC/B,MAAM,UAEL,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAClB,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE;YACvC,kBAAkB,CAAC,OAAO,CAAC;;YAAK,wBAAwB,CAAC,GAAG,CAAC,CACrD,CACZ,CAAC,CACS;QACb,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EACH,eAAe;gBACb,CAAC,CAAC,IAAI,wBAAwB,CAAC,kBAAkB,CAAC,KAAK,eAAe,EAAE;gBACxE,CAAC,CAAC,YAAY,EAElB,SAAS,EAAE;gBACT,KAAK,EAAE;oBACL,QAAQ,EAAE,IAAI;oBACd,OAAO,EAAE;wBACP,KAAK,EAAE,OAAO,CAAC,YAAY;qBAC5B;iBACF;aACF,GACD;QAEF,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,OAAO,GAAG,mBAAmB,CAAC;wBAClC,OAAO,EAAE,kBAAkB;wBAC3B,IAAI;wBACJ,YAAY,EAAE,gBAAgB,kBAAkB,CAAC,OAAO,CAAC,MAAM,wBAAwB,CAAC,kBAAkB,CAAC,MAAM,YAAY,EAAE;qBAChI,CAAC,CAAA;oBACF,OAAO,CAAC,cAAc,CAAC;wBACrB,YAAY,EAAE,QAAQ;wBACtB,aAAa;wBACb,YAAY;wBACZ,kBAAkB;wBAClB,eAAe;qBAChB,CAAC,CAAA;oBACF,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,QAAQ,EAAE,CAAC,eAAe,aAGnB;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACF,CACjB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.d.ts

@@ -1,26 +0,0 @@
-import { Feature } from '@jbrowse/core/util';
-export interface Feat {
-    start: number;
-    end: number;
-    type: string;
-}
-export declare function stitch(subfeats: Feat[], sequence: string): string;
-export declare function calculateProteinSequence({ cds, sequence, codonTable, }: {
-    cds: Feat[];
-    sequence: string;
-    codonTable: Record<string, string>;
-}): string;
-export declare function revlist(list: {
-    start: number;
-    end: number;
-    type: string;
-}[], seqlen: number): {
-    start: number;
-    end: number;
-    type: string;
-}[];
-export declare function dedupe(list: Feat[]): Feat[];
-export declare function getProteinSequence({ selectedTranscript, seq, }: {
-    seq: string;
-    selectedTranscript: Feature;
-}): string;

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js

@@ -1,48 +0,0 @@
-import { defaultCodonTable, generateCodonTable, revcom, } from '@jbrowse/core/util';
-export function stitch(subfeats, sequence) {
-    return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
-}
-export function calculateProteinSequence({ cds, sequence, codonTable, }) {
-    const str = stitch(cds, sequence);
-    let protein = '';
-    for (let i = 0; i < str.length; i += 3) {
-        // use & symbol for undefined codon, or partial slice
-        protein += codonTable[str.slice(i, i + 3)] ?? '&';
-    }
-    return protein;
-}
-export function revlist(list, seqlen) {
-    return list
-        .map(sub => ({
-        ...sub,
-        start: seqlen - sub.end,
-        end: seqlen - sub.start,
-    }))
-        .sort((a, b) => a.start - b.start);
-}
-// filter items if they have the same "ID" or location
-function getItemId(feat) {
-    return `${feat.start}-${feat.end}`;
-}
-// filters if successive elements share same start/end
-export function dedupe(list) {
-    return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
-}
-export function getProteinSequence({ selectedTranscript, seq, }) {
-    // @ts-expect-error
-    const f = selectedTranscript.toJSON();
-    const cds = dedupe(f.subfeatures
-        .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'));
-    return calculateProteinSequence({
-        cds: f.strand === -1 ? revlist(cds, seq.length) : cds,
-        sequence: f.strand === -1 ? revcom(seq) : seq,
-        codonTable: generateCodonTable(defaultCodonTable),
-    });
-}
-//# sourceMappingURL=calculateProteinSequence.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"calculateProteinSequence.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,iBAAiB,EACjB,kBAAkB,EAClB,MAAM,GACP,MAAM,oBAAoB,CAAA;AAQ3B,MAAM,UAAU,MAAM,CAAC,QAAgB,EAAE,QAAgB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACzE,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,GAAG,EACH,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACvC,qDAAqD;QACrD,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;IACnD,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,OAAO,CACrB,IAAoD,EACpD,MAAc;IAEd,OAAO,IAAI;SACR,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,MAAM,GAAG,GAAG,CAAC,GAAG;QACvB,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,KAAK;KACxB,CAAC,CAAC;SACF,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AACtC,CAAC;AAED,sDAAsD;AACtD,SAAS,SAAS,CAAC,IAAU;IAC3B,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACpC,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAY;IACjC,OAAO,IAAI,CAAC,MAAM,CAChB,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,SAAS,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,CAAE,CAAC,CACzE,CAAA;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,EACjC,kBAAkB,EAClB,GAAG,GAIJ;IACC,mBAAmB;IACnB,MAAM,CAAC,GAAG,kBAAkB,CAAC,MAAM,EAMlC,CAAA;IACD,MAAM,GAAG,GAAG,MAAM,CAChB,CAAC,CAAC,WAAW;SACV,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;SACjC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK;QAC1B,GAAG,EAAE,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK;KACvB,CAAC,CAAC;SACF,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,KAAK,CAAC,CACjC,CAAA;IAED,OAAO,wBAAwB,CAAC;QAC9B,GAAG,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG;QACrD,QAAQ,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG;QAC7C,UAAU,EAAE,kBAAkB,CAAC,iBAAiB,CAAC;KAClD,CAAC,CAAA;AACJ,CAAC"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.d.ts

@@ -1 +0,0 @@
-export { default } from './NcbiBlastPanel';

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js

@@ -1,2 +0,0 @@
-export { default } from './NcbiBlastPanel';
-//# sourceMappingURL=index.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/index.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAA"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"ncbiBlastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAKxD,MAAM,UAAU,mBAAmB,CAAC,EAClC,YAAY,EACZ,IAAI,EACJ,OAAO,GAKR;IACC,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QACzC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,aAAa,EAAE,GAAG;QAClB,SAAS,EAAE,GAAG;QACd,eAAe,EAAE,IAAI;QACrB,gBAAgB,EAAE,IAAI;QACtB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,eAAe,EAAE,0BAA0B;KAC5C,CAA8B,CAAA;AACjC,CAAC"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"useFeatureSequence.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE3C,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAiC,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAW9E,MAAM,OAAO,GAAG,OAAO,CAAA;AAEvB,KAAK,UAAU,QAAQ,CAAC,EACtB,KAAK,EACL,GAAG,EACH,OAAO,EACP,OAAO,EACP,YAAY,GAOb;IACC,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;IAC/C,MAAM,QAAQ,GAAG,MAAM,eAAe,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IACpE,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;IACvC,CAAC;IACD,MAAM,SAAS,GAAG,aAAa,CAAA;IAC/B,MAAM,KAAK,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;QACjE,aAAa,EAAE,OAAO,CAAC,QAAQ,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC;QACzD,SAAS;QACT,OAAO,EAAE;YACP;gBACE,KAAK;gBACL,GAAG;gBACH,OAAO,EAAE,QAAQ,CAAC,mBAAmB,CAAC,OAAO,CAAC;gBAC9C,YAAY;aACb;SACF;KACF,CAAC,CAAc,CAAA;IAChB,OAAQ,KAAK,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,CAAwB,IAAI,EAAE,CAAA;AAC3D,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,EACjC,IAAI,EACJ,OAAO,EACP,QAAQ,GAAG,CAAC,EACZ,SAAS,GAAG,IAAI,GAMjB;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAyB,CAAA;IACjE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,YAAY,GAAG,IAAI,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,CAAA;IAC7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,IAAI,EAAE,CAAC;YACT,mEAAmE;YACnE,CAAC;YAAA,CAAC,KAAK,IAAI,EAAE;gBACX,IAAI,CAAC;oBACH,QAAQ,CAAC,SAAS,CAAC,CAAA;oBACnB,WAAW,CAAC,SAAS,CAAC,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;oBAChC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,MAAM,EAI7C,CAAA;oBACD,IAAI,CAAC,YAAY,EAAE,CAAC;wBAClB,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;oBACtC,CAAC;oBACD,IAAI,CAAC,SAAS,IAAI,GAAG,GAAG,KAAK,GAAG,OAAO,EAAE,CAAC;wBACxC,WAAW,CAAC;4BACV,KAAK,EAAE,gCAAgC,OAAO,wCAAwC;yBACvF,CAAC,CAAA;oBACJ,CAAC;yBAAM,CAAC;wBACN,MAAM,CAAC,GAAG,KAAK,GAAG,QAAQ,CAAA;wBAC1B,MAAM,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAA;wBACxB,WAAW,CAAC;4BACV,GAAG,EAAE,MAAM,QAAQ,CAAC;gCAClB,KAAK;gCACL,GAAG;gCACH,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;4BACF,QAAQ,EAAE,MAAM,QAAQ,CAAC;gCACvB,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gCACrB,GAAG,EAAE,KAAK;gCACV,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;4BACF,UAAU,EAAE,MAAM,QAAQ,CAAC;gCACzB,KAAK,EAAE,GAAG;gCACV,GAAG,EAAE,CAAC;gCACN,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;yBACH,CAAC,CAAA;oBACJ,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;gBACb,CAAC;YACH,CAAC,CAAC,EAAE,CAAA;QACN,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,YAAY,EAAE,SAAS,CAAC,CAAC,CAAA;IACtD,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;AAC5B,CAAC"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/util.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,MAAM,CAAC,CAAyC;IAC9D,OAAO,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,CAAA;AAC3D,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,CAAS;IAC7B,OAAO,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;AAC3B,CAAC"}

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"}