jbrowse-plugin-msaview 2.3.8 → 2.4.1

package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx

@@ -1,123 +0,0 @@
-import React, { useState } from 'react'
-
-import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
-import { getContainingView, getSession } from '@jbrowse/core/util'
-import { Button, DialogActions, DialogContent, Link } from '@mui/material'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-import { ensemblGeneTreeLaunchView } from './ensemblGeneTreeLaunchView'
-import { useGeneTree } from './useGeneTree'
-import { getGeneDisplayName } from '../../util'
-import TranscriptSelector from '../TranscriptSelector'
-import { useTranscriptSelection } from '../useTranscriptSelection'
-
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
-const useStyles = makeStyles()({
-  dialogContent: {
-    width: '80em',
-    display: 'flex',
-    flexDirection: 'column',
-    gap: 16,
-  },
-})
-
-const EnsemblGeneTree = observer(function ({
-  model,
-  feature,
-  handleClose,
-}: {
-  model: AbstractTrackModel
-  feature: Feature
-  handleClose: () => void
-}) {
-  const session = getSession(model)
-  const view = getContainingView(model) as LinearGenomeViewModel
-  const { classes } = useStyles()
-  const [launchViewError, setLaunchViewError] = useState<unknown>()
-  const {
-    options,
-    selectedId,
-    setSelectedId,
-    selectedTranscript,
-    proteinSequence,
-    error: featureSequenceError,
-  } = useTranscriptSelection({ feature, view })
-  const { treeData, isTreeLoading, treeError } = useGeneTree(selectedId)
-
-  const loadingMessage = isTreeLoading
-    ? 'Loading tree data from Ensembl GeneTree'
-    : undefined
-  const e = treeError ?? launchViewError ?? featureSequenceError
-
-  return (
-    <>
-      <DialogContent className={classes.dialogContent}>
-        {e ? <ErrorMessage error={e} /> : null}
-        {loadingMessage ? <LoadingEllipses message={loadingMessage} /> : null}
-        {treeData ? (
-          <div>
-            <div>Found Ensembl Compara GeneTree: {treeData.geneTreeId}</div>
-            <Link
-              target="_blank"
-              href={`https://useast.ensembl.org/Multi/GeneTree/Image?gt=${treeData.geneTreeId}`}
-            >
-              See {treeData.geneTreeId} at Ensembl
-            </Link>
-          </div>
-        ) : null}
-
-        <TranscriptSelector
-          feature={feature}
-          options={options}
-          selectedId={selectedId}
-          selectedTranscript={selectedTranscript}
-          onTranscriptChange={setSelectedId}
-          proteinSequence={proteinSequence}
-        />
-      </DialogContent>
-
-      <DialogActions>
-        <Button
-          color="primary"
-          variant="contained"
-          onClick={() => {
-            try {
-              if (!treeData) {
-                return
-              }
-              setLaunchViewError(undefined)
-
-              ensemblGeneTreeLaunchView({
-                feature,
-                view,
-                session,
-                newViewTitle: getGeneDisplayName(feature),
-                data: treeData,
-              })
-              handleClose()
-            } catch (e) {
-              console.error(e)
-              setLaunchViewError(e)
-            }
-          }}
-        >
-          Submit
-        </Button>
-        <Button
-          color="secondary"
-          variant="contained"
-          onClick={() => {
-            handleClose()
-          }}
-        >
-          Cancel
-        </Button>
-      </DialogActions>
-    </>
-  )
-})
-
-export default EnsemblGeneTree

package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts

@@ -1,30 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util'
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
-export function ensemblGeneTreeLaunchView({
-  session,
-  newViewTitle,
-  view,
-  feature,
-  data,
-}: {
-  session: AbstractSessionModel
-  newViewTitle: string
-  view: LinearGenomeViewModel
-  feature: Feature
-  data: {
-    tree: string
-    msa: string
-    treeMetadata: string
-  }
-}) {
-  session.addView('MsaView', {
-    type: 'MsaView',
-    displayName: newViewTitle,
-    colWidth: 10,
-    rowHeight: 12,
-    data,
-    connectedViewId: view.id,
-    connectedFeature: feature.toJSON(),
-  })
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts

@@ -1,47 +0,0 @@
-import { gatherSequencesFromTree } from './gatherSequencesFromTree'
-import { fetchWithLocalStorageCache, jsonfetch, textfetch } from './util'
-
-import type { TreeNode } from './types'
-
-const base = 'https://rest.ensembl.org'
-
-export async function geneTreeFetcher(id2: string) {
-  const id = id2.replace(/\..*/, '')
-  const { species } = await fetchWithLocalStorageCache(`${id}-ensembl`, () =>
-    jsonfetch<{ species: string }>(
-      `${base}/lookup/id/${id}?content-type=application/json`,
-    ),
-  )
-  const treeBase = `${base}/genetree/member/id/${species}/${id}`
-  const geneTreeResult = await fetchWithLocalStorageCache(`${id}-msa`, () =>
-    jsonfetch<{ tree: TreeNode; id: string }>(
-      `${treeBase}?content-type=application/json;aligned=1;sequence=pep`,
-    ),
-  )
-
-  // we query again to get newick format tree. could probably extract from json
-  // as alternative
-  const tree = await fetchWithLocalStorageCache<string>(`${id}-tree`, () =>
-    textfetch(`${treeBase}?nh_format=simple;content-type=text/x-nh`),
-  )
-
-  const res = gatherSequencesFromTree(geneTreeResult.tree)
-  return {
-    geneTreeId: geneTreeResult.id,
-    tree,
-    msa: res.map(r => `>${r.id}\n${r.seq}`).join('\n'),
-    treeMetadata: JSON.stringify(
-      Object.fromEntries(
-        res.map(
-          r =>
-            [
-              r.id,
-              {
-                genome: r.species,
-              },
-            ] as const,
-        ),
-      ),
-    ),
-  }
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.ts

@@ -1,22 +0,0 @@
-import type { TreeNode, TreeRow } from './types'
-
-export function gatherSequencesFromTree(tree: TreeNode, arr: TreeRow[] = []) {
-  if (tree.children) {
-    for (const child of tree.children) {
-      if (child.sequence) {
-        const id = child.sequence.id[0]?.accession
-        if (id) {
-          arr.push({
-            id,
-            seq: child.sequence.mol_seq.seq,
-            species:
-              child.taxonomy.common_name || child.taxonomy.scientific_name,
-            genomicLocString: child.sequence.mol_seq.location,
-          })
-        }
-      }
-      gatherSequencesFromTree(child, arr)
-    }
-  }
-  return arr
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/types.ts

@@ -1,28 +0,0 @@
-export interface TreeNodeSequence {
-  mol_seq: {
-    seq: string
-    location?: string
-  }
-  id: {
-    accession: string
-  }[]
-}
-
-export interface TreeNodeTaxonomy {
-  common_name: string
-  scientific_name: string
-}
-
-// This is a self-referential tree data structure
-export interface TreeNode {
-  children?: TreeNode[]
-  sequence?: TreeNodeSequence
-  taxonomy: TreeNodeTaxonomy
-}
-
-export interface TreeRow {
-  id: string
-  seq: string
-  species: string
-  genomicLocString?: string
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts

@@ -1,17 +0,0 @@
-import useSWR from 'swr'
-
-import { geneTreeFetcher } from './ensemblGeneTreeUtils'
-
-export function useGeneTree(geneId: string) {
-  const { data, error, isLoading } = useSWR(
-    () => (geneId ? ['geneTree', geneId] : null),
-    ([, geneId]) => geneTreeFetcher(geneId),
-    {
-      revalidateOnFocus: false,
-      revalidateOnReconnect: false,
-      revalidateIfStale: false,
-    },
-  )
-
-  return { treeData: data, isTreeLoading: isLoading, treeError: error }
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/util.ts

@@ -1,6 +0,0 @@
-export {
-  fetchWithLocalStorageCache,
-  jsonfetch,
-  textfetch,
-  unzipfetch,
-} from '../../../utils/fetch'