jbrowse-plugin-msaview 2.0.6 → 2.2.0

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/dist/OpenInNewIcon.d.ts

@@ -1,3 +0,0 @@
-import React from 'react';
-import type { SvgIconProps } from '@mui/material';
-export default function OpenInNewIcon(props: SvgIconProps): React.JSX.Element;

package/dist/OpenInNewIcon.js

@@ -1,8 +0,0 @@
-import React from 'react';
-import { SvgIcon } from '@mui/material';
-export default function OpenInNewIcon(props) {
-    return (React.createElement(SvgIcon, { ...props },
-        React.createElement("path", { d: "M0 0h24v24H0z", fill: "none" }),
-        React.createElement("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" })));
-}
-//# sourceMappingURL=OpenInNewIcon.js.map

package/dist/OpenInNewIcon.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"OpenInNewIcon.js","sourceRoot":"","sources":["../src/OpenInNewIcon.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAIvC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,KAAmB;IACvD,OAAO,CACL,oBAAC,OAAO,OAAK,KAAK;QAChB,8BAAM,CAAC,EAAC,eAAe,EAAC,IAAI,EAAC,MAAM,GAAG;QACtC,8BAAM,CAAC,EAAC,oIAAoI,GAAG,CACvI,CACX,CAAA;AACH,CAAC"}

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/calculateProteinSequence.ts

@@ -1,92 +0,0 @@
-import {
-  Feature,
-  defaultCodonTable,
-  generateCodonTable,
-  revcom,
-} from '@jbrowse/core/util'
-
-export interface Feat {
-  start: number
-  end: number
-  type: string
-}
-
-export function stitch(subfeats: Feat[], sequence: string) {
-  return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('')
-}
-
-export function calculateProteinSequence({
-  cds,
-  sequence,
-  codonTable,
-}: {
-  cds: Feat[]
-  sequence: string
-  codonTable: Record<string, string>
-}) {
-  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: { start: number; end: number; type: string }[],
-  seqlen: number,
-) {
-  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: Feat) {
-  return `${feat.start}-${feat.end}`
-}
-
-// filters if successive elements share same start/end
-export function dedupe(list: Feat[]) {
-  return list.filter(
-    (item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]!),
-  )
-}
-
-export function getProteinSequence({
-  selectedTranscript,
-  seq,
-}: {
-  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 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),
-  })
-}

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

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

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}`,
-  }
-}

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>
-  )
-}