jbrowse-plugin-protein3d 0.0.2 → 0.0.3

package/dist/LaunchProteinView/components/PreLoadedStructureMapping.js

@@ -1,72 +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 { 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, map) {
-    return (map.get(stripTrailingVersion(f?.get('name')) ?? '') ??
-        map.get(stripTrailingVersion(f?.get('id')) ?? ''));
-}
-const AutoForm = observer(function AutoForm({ model, feature, handleClose, }) {
-    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 (React.createElement(React.Fragment, null,
-        React.createElement(DialogContent, { className: classes.dialogContent },
-            React.createElement("div", { className: classes.section }, error ? (React.createElement(ErrorMessage, { error: error })) : data ? (React.createElement("div", null,
-                React.createElement(Intro, null),
-                hasDataForFeatures.length === 0 ? (React.createElement(Typography, { color: "error" }, "No data for feature")) : (React.createElement(React.Fragment, null,
-                    React.createElement("div", { className: classes.section },
-                        React.createElement(TextField, { value: userSelection, onChange: event => setUserSelection(event.target.value), label: "Choose isoform", select: true }, hasDataForFeatures.map(val => (React.createElement(MenuItem, { value: val.id(), key: val.id() },
-                            getDisplayName(val),
-                            " (has data)"))))))))) : (React.createElement(LoadingEllipses, null)))),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel"),
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    session.addView('ProteinView', {
-                        type: 'ProteinView',
-                        url,
-                        mapping,
-                    });
-                    handleClose();
-                } }, "Submit"))));
-});
-function Intro() {
-    return (React.createElement("div", null,
-        "Find structure associated with gene ID:",
-        ' ',
-        React.createElement(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)")));
-}
-export default AutoForm;
-//# sourceMappingURL=PreLoadedStructureMapping.js.map

package/dist/LaunchProteinView/components/PreLoadedStructureMapping.js.map

@@ -1 +0,0 @@
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package/dist/LaunchProteinView/components/useCheckAlphaFoldDBExistence.d.ts

@@ -1,7 +0,0 @@
-export declare function useCheckAlphaFoldDBExistence({ foundStructureId, }: {
-    foundStructureId?: string;
-}): {
-    error: unknown;
-    loading: boolean;
-    success: boolean;
-};

package/dist/LaunchProteinView/components/useCheckAlphaFoldDBExistence.js

@@ -1,26 +0,0 @@
-import { useEffect, useState } from 'react';
-export function useCheckAlphaFoldDBExistence({ foundStructureId, }) {
-    const [error, setError] = useState();
-    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 };
-}
-//# sourceMappingURL=useCheckAlphaFoldDBExistence.js.map

package/dist/LaunchProteinView/components/useCheckAlphaFoldDBExistence.js.map

@@ -1 +0,0 @@
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package/dist/LaunchProteinView/useMyGeneInfo.js.map

@@ -1 +0,0 @@
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package/dist/LaunchProteinView/useProteinSequences.d.ts

@@ -1,10 +0,0 @@
-import { Feature } from '@jbrowse/core/util';
-export default function useAllSequences({ feature, view, }: {
-    feature: Feature;
-    view: {
-        assemblyNames?: string[];
-    } | undefined;
-}): {
-    seqs: Record<string, string> | undefined;
-    error: unknown;
-};

package/dist/LaunchProteinView/useProteinSequences.js.map

@@ -1 +0,0 @@
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package/dist/LaunchProteinView/util.js.map

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package/dist/ProteinModelSessionExtension.d.ts

@@ -1,11 +0,0 @@
-import { Row } from './LaunchProteinView/util';
-declare const ProteinModelSessionExtension: import("mobx-state-tree").IModelType<{}, {
-    data: Row[] | undefined;
-    error: unknown;
-} & {
-    setData(a?: Row[]): void;
-    setError(e: unknown): void;
-} & {
-    afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export default ProteinModelSessionExtension;

package/dist/ProteinModelSessionExtension.js

@@ -1,53 +0,0 @@
-import { addDisposer, types } from 'mobx-state-tree';
-import { autorun } from 'mobx';
-import { ungzip } from 'pako';
-import { abfetch } from './fetchUtils';
-const ProteinModelSessionExtension = types
-    .model({})
-    .volatile(() => ({
-    data: undefined,
-    error: undefined,
-}))
-    .actions(self => ({
-    setData(a) {
-        self.data = a;
-    },
-    setError(e) {
-        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;
-//# sourceMappingURL=ProteinModelSessionExtension.js.map

package/dist/ProteinModelSessionExtension.js.map

@@ -1 +0,0 @@
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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