jbrowse-plugin-protein3d 0.0.2 → 0.0.4

package/src/LaunchProteinView/components/PreLoadedStructureMapping.tsx

@@ -1,153 +0,0 @@
-import React, { useEffect, useMemo, useState } from 'react'
-import { observer } from 'mobx-react'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  Link,
-  MenuItem,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
-import { AbstractTrackModel, Feature, getSession } from '@jbrowse/core/util'
-
-// locals
-import {
-  createMapFromData,
-  getDisplayName,
-  getTranscriptFeatures,
-  stripTrailingVersion,
-} from '../util'
-import { genomeToTranscriptMapping } from '../../genomeToTranscriptMapping'
-
-const useStyles = makeStyles()(theme => ({
-  section: {
-    marginTop: theme.spacing(6),
-  },
-
-  dialogContent: {
-    width: '80em',
-  },
-}))
-
-function foundF(f: Feature | undefined, map: Map<string, string>) {
-  return (
-    map.get(stripTrailingVersion(f?.get('name')) ?? '') ??
-    map.get(stripTrailingVersion(f?.get('id')) ?? '')
-  )
-}
-
-const AutoForm = observer(function AutoForm({
-  model,
-  feature,
-  handleClose,
-}: {
-  model: AbstractTrackModel
-  feature: Feature
-  handleClose: () => void
-}) {
-  const { classes } = useStyles()
-  const session = getSession(model)
-  // @ts-expect-error
-  const { proteinModel } = session
-  const { data, error } = proteinModel
-  // check if we are looking at a 'two-level' or 'three-level' feature by
-  // finding exon/CDS subfeatures. we want to select from transcript names
-  const options = getTranscriptFeatures(feature)
-  const transcriptIdToStructureMap = useMemo(
-    () => createMapFromData(data),
-    [data],
-  )
-
-  const hasDataForFeatures = useMemo(
-    () => options.filter(f => foundF(f, transcriptIdToStructureMap)),
-    [transcriptIdToStructureMap, options],
-  )
-  const [userSelection, setUserSelection] = useState('')
-  const userSelectionFeat = options.find(f => f.id() === userSelection)
-  const foundStructureId = foundF(userSelectionFeat, transcriptIdToStructureMap)
-
-  useEffect(() => {
-    setUserSelection(hasDataForFeatures[0]?.id())
-  }, [hasDataForFeatures])
-
-  const mapping =
-    foundStructureId && userSelectionFeat
-      ? genomeToTranscriptMapping(userSelectionFeat)
-      : []
-  const url = foundStructureId
-    ? `https://files.rcsb.org/view/${foundStructureId}.cif`
-    : undefined
-
-  return (
-    <>
-      <DialogContent className={classes.dialogContent}>
-        <div className={classes.section}>
-          {error ? (
-            <ErrorMessage error={error} />
-          ) : data ? (
-            <div>
-              <Intro />
-              {hasDataForFeatures.length === 0 ? (
-                <Typography color="error">No data for feature</Typography>
-              ) : (
-                <>
-                  <div className={classes.section}>
-                    <TextField
-                      value={userSelection}
-                      onChange={event => setUserSelection(event.target.value)}
-                      label="Choose isoform"
-                      select
-                    >
-                      {hasDataForFeatures.map(val => (
-                        <MenuItem value={val.id()} key={val.id()}>
-                          {getDisplayName(val)} (has data)
-                        </MenuItem>
-                      ))}
-                    </TextField>
-                  </div>
-                </>
-              )}
-            </div>
-          ) : (
-            <LoadingEllipses />
-          )}
-        </div>
-      </DialogContent>
-      <DialogActions>
-        <Button variant="contained" color="secondary" onClick={handleClose}>
-          Cancel
-        </Button>
-        <Button
-          variant="contained"
-          color="primary"
-          onClick={() => {
-            session.addView('ProteinView', {
-              type: 'ProteinView',
-              url,
-              mapping,
-            })
-            handleClose()
-          }}
-        >
-          Submit
-        </Button>
-      </DialogActions>
-    </>
-  )
-})
-
-function Intro() {
-  return (
-    <div>
-      Find structure associated with gene ID:{' '}
-      <Link href="http://useast.ensembl.org/biomart/martview/4b20effd49654183333b81e98757976f?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id_version|hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id|hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id_version|hsapiens_gene_ensembl.default.feature_page.pdb|hsapiens_gene_ensembl.default.feature_page.refseq_mrna|hsapiens_gene_ensembl.default.feature_page.refseq_mrna_predicted&FILTERS=&VISIBLEPANEL=attributepanel">
-        Human mappings generated from BioMart (April 13, 2023)
-      </Link>
-    </div>
-  )
-}
-
-export default AutoForm

package/src/LaunchProteinView/components/useCheckAlphaFoldDBExistence.ts

@@ -1,31 +0,0 @@
-import { useEffect, useState } from 'react'
-
-export function useCheckAlphaFoldDBExistence({
-  foundStructureId,
-}: {
-  foundStructureId?: string
-}) {
-  const [error, setError] = useState<unknown>()
-  const [loading, setLoading] = useState(false)
-  const [success, setSuccess] = useState(false)
-  useEffect(() => {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
-      try {
-        if (foundStructureId) {
-          setLoading(true)
-          await fetch(
-            `https://alphafold.ebi.ac.uk/files/AF-${foundStructureId}-F1-model_v4.cif`,
-            { method: 'HEAD' },
-          )
-          setLoading(false)
-          setSuccess(true)
-        }
-      } catch (e) {
-        console.error(e)
-        setError(e)
-      }
-    })()
-  }, [foundStructureId])
-  return { error, loading, success }
-}

package/src/ProteinModelSessionExtension.ts

@@ -1,71 +0,0 @@
-import { addDisposer, types } from 'mobx-state-tree'
-import { autorun } from 'mobx'
-import { ungzip } from 'pako'
-
-// locals
-import { Row } from './LaunchProteinView/util'
-import { abfetch } from './fetchUtils'
-
-const ProteinModelSessionExtension = types
-  .model({})
-  .volatile(() => ({
-    data: undefined as Row[] | undefined,
-    error: undefined as unknown,
-  }))
-  .actions(self => ({
-    setData(a?: Row[]) {
-      self.data = a
-    },
-    setError(e: unknown) {
-      self.error = e
-    },
-  }))
-  .actions(self => {
-    return {
-      afterCreate() {
-        const url = 'https://jbrowse.org/demos/protein3d/mart_export.txt.gz'
-        addDisposer(
-          self,
-          autorun(async () => {
-            try {
-              const ret = new TextDecoder('utf8').decode(
-                ungzip(await abfetch(url)),
-              )
-              const d = ret
-                .split('\n')
-                .slice(1)
-                .filter(line => !!line)
-                .map(line => {
-                  const res = line.split('\t')
-                  const [
-                    gene_id,
-                    gene_id_version,
-                    transcript_id,
-                    transcript_id_version,
-                    pdb_id,
-                    refseq_mrna_id,
-                    refseq_mrna_predicted_id,
-                  ] = res
-
-                  return {
-                    gene_id,
-                    gene_id_version,
-                    transcript_id_version,
-                    transcript_id,
-                    pdb_id,
-                    refseq_mrna_predicted_id,
-                    refseq_mrna_id,
-                  }
-                })
-
-              self.setData(d)
-            } catch (error) {
-              self.setError(error)
-            }
-          }),
-        )
-      },
-    }
-  })
-
-export default ProteinModelSessionExtension

package/src/ProteinView/useProteinViewClickBehavior.ts

@@ -1,48 +0,0 @@
-import { useEffect, useState } from 'react'
-import { getSession } from '@jbrowse/core/util'
-import { PluginContext } from 'molstar/lib/mol-plugin/context'
-
-// local
-import { JBrowsePluginProteinViewModel } from './model'
-import { clickProteinToGenome } from './proteinToGenomeMapping'
-import {
-  StructureElement,
-  StructureProperties as Props,
-} from 'molstar/lib/mol-model/structure'
-
-export default function useProteinViewClickActionBehavior({
-  plugin,
-  model,
-}: {
-  plugin?: PluginContext
-  model: JBrowsePluginProteinViewModel
-}) {
-  const [error, setError] = useState<unknown>()
-  const session = getSession(model)
-  useEffect(() => {
-    if (!plugin) {
-      return
-    }
-    plugin.behaviors.interaction.click.subscribe(event => {
-      if (StructureElement.Loci.is(event.current.loci)) {
-        const loc = StructureElement.Loci.getFirstLocation(event.current.loci)
-        if (loc) {
-          const pos = Props.residue.auth_seq_id(loc)
-          const code = Props.atom.label_comp_id(loc)
-          const chain = Props.chain.auth_asym_id(loc)
-          model.setHoveredPosition({
-            structureSeqPos: pos - 1,
-            code,
-            chain,
-          })
-
-          clickProteinToGenome({ model, structureSeqPos: pos - 1 }).catch(e => {
-            console.error(e)
-            setError(e)
-          })
-        }
-      }
-    })
-  }, [plugin, session, model])
-  return { error }
-}

package/src/ProteinView/useProteinViewHoverBehavior.ts

@@ -1,44 +0,0 @@
-import { useEffect } from 'react'
-import { getSession } from '@jbrowse/core/util'
-import { PluginContext } from 'molstar/lib/mol-plugin/context'
-
-// local
-import { JBrowsePluginProteinViewModel } from './model'
-import {
-  StructureElement,
-  StructureProperties as Props,
-} from 'molstar/lib/mol-model/structure'
-import { hoverProteinToGenome } from './proteinToGenomeMapping'
-
-export default function useProteinViewClickActionBehavior({
-  plugin,
-  model,
-}: {
-  plugin?: PluginContext
-  model: JBrowsePluginProteinViewModel
-}) {
-  const session = getSession(model)
-  useEffect(() => {
-    if (!plugin) {
-      return
-    }
-    plugin.behaviors.interaction.hover.subscribe(event => {
-      if (StructureElement.Loci.is(event.current.loci)) {
-        const loc = StructureElement.Loci.getFirstLocation(event.current.loci)
-        if (loc) {
-          // example code for this label
-          // https://github.com/molstar/molstar/blob/60550cfea1f62a50a764d5714307d6d1049be71d/src/mol-theme/label.ts#L255-L264
-          const structureSeqPos = Props.residue.auth_seq_id(loc)
-          const code = Props.atom.label_comp_id(loc)
-          const chain = Props.chain.auth_asym_id(loc)
-          model.setHoveredPosition({
-            structureSeqPos: structureSeqPos - 1,
-            code,
-            chain,
-          })
-          hoverProteinToGenome({ model, structureSeqPos: structureSeqPos - 1 })
-        }
-      }
-    })
-  }, [plugin, session, model])
-}