jbrowse-plugin-msaview 2.1.0 → 2.2.0

package/src/LaunchMsaView/components/MSALoader/MSALoader.tsx

@@ -1,130 +0,0 @@
-import React, { useEffect, useState } from 'react'
-
-import { FileSelector } from '@jbrowse/core/ui'
-import {
-  AbstractTrackModel,
-  Feature,
-  FileLocation,
-  getContainingView,
-  getSession,
-} from '@jbrowse/core/util'
-import { openLocation } from '@jbrowse/core/util/io'
-import { Button, DialogActions, DialogContent } from '@mui/material'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-import { fetchGeneList } from './fetchGeneList'
-import { preCalculatedLaunchView } from './preCalculatedLaunchView'
-import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util'
-
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
-const useStyles = makeStyles()({
-  dialogContent: {
-    width: '80em',
-  },
-})
-
-const PreLoadedMSA = observer(function PreLoadedMSA2({
-  model,
-  feature,
-  handleClose,
-}: {
-  model: AbstractTrackModel
-  feature: Feature
-  handleClose: () => void
-}) {
-  const session = getSession(model)
-  const view = getContainingView(model) as LinearGenomeViewModel
-  const { classes } = useStyles()
-  const [, setError] = useState<unknown>()
-  const [geneNameList, setGeneNameList] = useState<string[]>()
-  const [fileLocation, setFileLocation] = useState<FileLocation>()
-
-  useEffect(() => {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
-      try {
-        const data = await fetchGeneList()
-        setGeneNameList(data)
-        const set = new Set(data)
-        const options = getTranscriptFeatures(feature)
-        const ret = options.find(val => set.has(getId(val)))
-        if (ret) {
-          setUserSelection(getId(ret))
-        }
-      } catch (e) {
-        console.error(e)
-        setError(e)
-      }
-    })()
-  }, [feature])
-
-  useEffect(() => {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
-      try {
-        if (fileLocation) {
-          await openLocation(fileLocation).readFile()
-        }
-      } catch (e) {
-        console.error(e)
-        setError(e)
-      }
-    })()
-  }, [fileLocation, feature])
-
-  const set = new Set(geneNameList)
-  const options = getTranscriptFeatures(feature)
-  const ret = options.find(val => set.has(getId(val)))
-  const [userSelection, setUserSelection] = useState(getId(options[0]))
-
-  return (
-    <>
-      <DialogContent className={classes.dialogContent}>
-        <FileSelector location={fileLocation} setLocation={setFileLocation} />
-      </DialogContent>
-
-      <DialogActions>
-        <Button
-          color="primary"
-          variant="contained"
-          onClick={() => {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
-            ;(async () => {
-              try {
-                if (!ret) {
-                  return
-                }
-                await preCalculatedLaunchView({
-                  userSelection,
-                  session,
-                  newViewTitle: getGeneDisplayName(ret),
-                  view,
-                  feature: ret,
-                })
-                handleClose()
-              } catch (e) {
-                console.error(e)
-                setError(e)
-              }
-            })()
-          }}
-        >
-          Submit
-        </Button>
-        <Button
-          color="secondary"
-          variant="contained"
-          onClick={() => {
-            handleClose()
-          }}
-        >
-          Cancel
-        </Button>
-      </DialogActions>
-    </>
-  )
-})
-
-export default PreLoadedMSA

package/src/LaunchMsaView/components/MSALoader/fetchGeneList.ts

@@ -1,13 +0,0 @@
-export async function fetchGeneList() {
-  const res = await fetch(
-    'https://jbrowse.org/demos/msaview/knownCanonical/list.txt',
-  )
-  if (!res.ok) {
-    throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`)
-  }
-  const result = await res.text()
-  return result
-    .split('\n')
-    .map(f => f.trim())
-    .filter(f => !!f)
-}

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

@@ -1,55 +0,0 @@
-import { AbstractSessionModel, Feature } from '@jbrowse/core/util'
-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) {
-    throw new Error(`HTTP ${res.status} fetching ${await res.text()}`)
-  }
-  const data = await res.arrayBuffer()
-  return new TextDecoder().decode(ungzip(data))
-}
-
-export async function preCalculatedLaunchView({
-  userSelection,
-  session,
-  newViewTitle,
-  view,
-  feature,
-}: {
-  session: AbstractSessionModel
-  userSelection: string
-  newViewTitle: string
-  view: LinearGenomeViewModel
-  feature: Feature
-}) {
-  const d = await myfetch(
-    `https://jbrowse.org/demos/msaview/knownCanonical/${userSelection}.mfa.gz`,
-  )
-
-  session.addView('MsaView', {
-    type: 'MsaView',
-    displayName: newViewTitle,
-    treeAreaWidth: 200,
-    treeWidth: 100,
-    drawNodeBubbles: false,
-    labelsAlignRight: true,
-    showBranchLen: false,
-    colWidth: 10,
-    rowHeight: 12,
-    colorSchemeName: 'percent_identity_dynamic',
-    treeFilehandle: {
-      uri: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.nh',
-    },
-    treeMetadataFilehandle: {
-      uri: 'https://s3.amazonaws.com/jbrowse.org/demos/app/species.json',
-    },
-    data: {
-      msa: d,
-    },
-    connectedViewId: view.id,
-    connectedFeature: feature.toJSON(),
-  })
-}

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

@@ -1,171 +0,0 @@
-import React, { useState } from 'react'
-
-import { ErrorMessage } from '@jbrowse/core/ui'
-import {
-  AbstractTrackModel,
-  Feature,
-  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'
-
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
-const useStyles = makeStyles()({
-  dialogContent: {
-    width: '80em',
-  },
-  textAreaFont: {
-    fontFamily: 'Courier New',
-  },
-})
-
-const NcbiBlastPanel = observer(function NcbiBlastPanel2({
-  handleClose,
-  feature,
-  model,
-}: {
-  model: AbstractTrackModel
-  feature: Feature
-  handleClose: () => void
-}) {
-  const { classes } = useStyles()
-  const view = getContainingView(model) as LinearGenomeViewModel
-  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 (
-    <DialogContent className={classes.dialogContent}>
-      {error ? <ErrorMessage error={error} /> : null}
-      <TextField2
-        value={blastDatabase}
-        onChange={event => {
-          setBlastDatabase(event.target.value)
-        }}
-        label="BLAST blastDatabase"
-        select
-      >
-        {blastDatabaseOptions.map(val => (
-          <MenuItem value={val} key={val}>
-            {val}
-          </MenuItem>
-        ))}
-      </TextField2>
-
-      <TextField2
-        value={msaAlgorithm}
-        onChange={event => {
-          setMsaAlgorithm(event.target.value)
-        }}
-        label="MSA Algorithm"
-        select
-      >
-        {msaAlgorithms.map(val => (
-          <MenuItem value={val} key={val}>
-            {val}
-          </MenuItem>
-        ))}
-      </TextField2>
-
-      <TextField2
-        value={userSelection}
-        onChange={event => {
-          setUserSelection(event.target.value)
-        }}
-        label="Choose isoform to BLAST"
-        select
-      >
-        {options.map(val => (
-          <MenuItem value={getId(val)} key={val.id()}>
-            {getGeneDisplayName(feature)} - {getTranscriptDisplayName(val)}
-          </MenuItem>
-        ))}
-      </TextField2>
-      <TextField2
-        variant="outlined"
-        multiline
-        minRows={5}
-        maxRows={10}
-        fullWidth
-        value={
-          proteinSequence
-            ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
-            : 'Loading...'
-        }
-        slotProps={{
-          input: {
-            readOnly: true,
-            classes: {
-              input: classes.textAreaFont,
-            },
-          },
-        }}
-      />
-
-      <DialogActions>
-        <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
-        </Button>
-        <Button
-          color="secondary"
-          variant="contained"
-          onClick={() => {
-            handleClose()
-          }}
-        >
-          Cancel
-        </Button>
-      </DialogActions>
-    </DialogContent>
-  )
-})
-
-export default NcbiBlastPanel

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

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

package/src/OpenInNewIcon.tsx

@@ -1,14 +0,0 @@
-import React from 'react'
-
-import { SvgIcon } from '@mui/material'
-
-import type { SvgIconProps } from '@mui/material'
-
-export default function OpenInNewIcon(props: SvgIconProps) {
-  return (
-    <SvgIcon {...props}>
-      <path d="M0 0h24v24H0z" fill="none" />
-      <path d="M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z" />
-    </SvgIcon>
-  )
-}