jbrowse-plugin-protein3d 0.0.2 → 0.0.4

package/src/index.ts

@@ -1,12 +1,14 @@
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { types } from 'mobx-state-tree'
+
 // locals
 import { version } from '../package.json'
 import ProteinViewF from './ProteinView'
 import LaunchProteinViewF from './LaunchProteinView'
 import AddHighlightModelF from './AddHighlightModel'
-import ProteinModelSessionExtension from './ProteinModelSessionExtension'
+import AlphaFoldConfidenceAdapterF from './AlphaFoldConfidenceAdapter'
+import UniProtVariationAdapterF from './UniProtVariationAdapter'
+import AlphaMissensePathogenicityAdapterF from './AlphaMissensePathogenicityAdapter'
 
 export default class ProteinViewer extends Plugin {
   name = 'ProteinViewer'
@@ -16,16 +18,9 @@ export default class ProteinViewer extends Plugin {
     ProteinViewF(pluginManager)
     LaunchProteinViewF(pluginManager)
     AddHighlightModelF(pluginManager)
-
-    pluginManager.addToExtensionPoint('Core-extendSession', session => {
-      return types.compose(
-        types.model({
-          proteinModel: types.optional(ProteinModelSessionExtension, {}),
-        }),
-        // @ts-expect-error
-        session,
-      )
-    })
+    AlphaFoldConfidenceAdapterF(pluginManager)
+    AlphaMissensePathogenicityAdapterF(pluginManager)
+    UniProtVariationAdapterF(pluginManager)
   }
 
   configure(_pluginManager: PluginManager) {}

package/src/mappings.test.ts

@@ -1,22 +1,24 @@
+import { expect, test } from 'vitest'
 import {
   genomeToTranscriptSeqMapping,
   structureSeqVsTranscriptSeqMap,
 } from './mappings'
 import { SimpleFeature } from '@jbrowse/core/util'
-import { feature, alignment } from './test_data/gene'
+import { feature, pairwiseAlignment } from './test_data/gene'
 
 test('test', () => {
-  const ret = structureSeqVsTranscriptSeqMap(alignment)
+  const ret = structureSeqVsTranscriptSeqMap(pairwiseAlignment)
   expect(ret).toMatchSnapshot()
 })
 
 test('mapping', () => {
+  // @ts-expect-error
   const res = genomeToTranscriptSeqMapping(new SimpleFeature(feature))
   const { p2g } = res
-  const aln = structureSeqVsTranscriptSeqMap(alignment)
+  const aln = structureSeqVsTranscriptSeqMap(pairwiseAlignment)
 
   // expected position in sequence
-  const s2 = alignment.alns[1].seq
+  const s2 = pairwiseAlignment.alns[1].seq
   expect(s2[392]).toBe('M')
   expect(s2[393]).toBe('K')
   expect(s2[394]).toBe('A')
@@ -24,7 +26,7 @@ test('mapping', () => {
   // maps the 392 position in the "pdb version of the protein" to the 0th
   // position in the genome version of the protein, and then maps that back to
   // the genome
-  const p0 = aln.structureSeqToTranscriptSeqPosition[392]!
+  const p0 = aln.transcriptSeqToStructureSeqPosition[392]!
   const g0 = p2g[p0]
   expect(p0).toBe(0)
   expect(g0).toBe(51_296_155)

package/src/mappings.ts

@@ -1,30 +1,27 @@
 import { Feature } from '@jbrowse/core/util'
 import { genomeToTranscriptSeqMapping as g2p } from 'g2p_mapper'
-
-export interface Alignment {
-  alns: {
-    id: string
-    seq: string
-  }[]
+export interface AlignmentRow {
+  id: string
+  seq: string
+}
+export interface PairwiseAlignment {
+  consensus: string
+  alns: readonly [AlignmentRow, AlignmentRow]
 }
 
-export function structureSeqVsTranscriptSeqMap(alignment: Alignment) {
-  const structureSeq = alignment.alns[0].seq
-  const transcriptSeq = alignment.alns[1].seq
+export function structureSeqVsTranscriptSeqMap(
+  pairwiseAlignment: PairwiseAlignment,
+) {
+  const structureSeq = pairwiseAlignment.alns[1].seq
+  const transcriptSeq = pairwiseAlignment.alns[0].seq
   if (structureSeq.length !== transcriptSeq.length) {
     throw new Error('mismatched length')
   }
 
   let j = 0
   let k = 0
-  const structureSeqToTranscriptSeqPosition = {} as Record<
-    string,
-    number | undefined
-  >
-  const transcriptSeqToStructureSeqPosition = {} as Record<
-    string,
-    number | undefined
-  >
+  const structureSeqToTranscriptSeqPosition = {} as Record<string, number>
+  const transcriptSeqToStructureSeqPosition = {} as Record<string, number>
 
   // eslint-disable-next-line unicorn/no-for-loop
   for (let i = 0; i < structureSeq.length; i++) {
@@ -48,15 +45,18 @@ export function structureSeqVsTranscriptSeqMap(alignment: Alignment) {
       j++
     }
   }
+
   return {
     structureSeqToTranscriptSeqPosition,
     transcriptSeqToStructureSeqPosition,
   }
 }
 
-export function structurePositionToAlignmentMap(alignment: Alignment) {
-  const structureSeq = alignment.alns[0].seq
-  const structurePositionToAlignment = {} as Record<string, number | undefined>
+export function structurePositionToAlignmentMap(
+  pairwiseAlignment: PairwiseAlignment,
+) {
+  const structureSeq = pairwiseAlignment.alns[1].seq
+  const structurePositionToAlignment = {} as Record<string, number>
 
   for (let i = 0, j = 0; i < structureSeq.length; i++) {
     if (structureSeq[i] !== '-') {
@@ -68,9 +68,11 @@ export function structurePositionToAlignmentMap(alignment: Alignment) {
   return structurePositionToAlignment
 }
 
-export function transcriptPositionToAlignmentMap(alignment: Alignment) {
-  const transcriptSeq = alignment.alns[1].seq
-  const transcriptPositionToAlignment = {} as Record<string, number | undefined>
+export function transcriptPositionToAlignmentMap(
+  pairwiseAlignment: PairwiseAlignment,
+) {
+  const transcriptSeq = pairwiseAlignment.alns[0].seq
+  const transcriptPositionToAlignment = {} as Record<string, number>
 
   for (let i = 0, j = 0; i < transcriptSeq.length; i++) {
     if (transcriptSeq[i] !== '-') {

package/src/test_data/gene.ts

@@ -586,9 +586,9 @@ export const feature = {
   uniqueId: '590611027-offset-601794870-0',
   parentId: '590611027-offset-601794870',
   __jbrowsefmt: {},
-}
+} as const
 
-export const alignment = {
+export const pairwiseAlignment = {
   consensus:
     '                                                                                                                                                                                                                                                                                                                                                                                                        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ',
   alns: [
@@ -601,4 +601,4 @@ export const alignment = {
       seq: '--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNPISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIITKAEEMLEKGPENEYSVDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALLELALLLMEQDRNEEAIKLLESAKQNYKNYSMESRTHFRIQAATLQAKSSLENSSRSMVSSVSL*',
     },
   ],
-}
+} as const

package/dist/LaunchProteinView/calculateProteinSequence.js.map

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

@@ -1,8 +0,0 @@
-import React from 'react';
-import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const AutoForm: ({ model, feature, handleClose, }: {
-    model: AbstractTrackModel;
-    feature: Feature;
-    handleClose: () => void;
-}) => React.JSX.Element;
-export default AutoForm;

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

@@ -1 +0,0 @@
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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/dist/ProteinView/components/Header.js.map

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package/dist/ProteinView/loadStructureFromData.js.map

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package/dist/ProteinView/loadStructureFromURL.js.map

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package/dist/ProteinView/useProteinViewClickBehavior.d.ts

@@ -1,8 +0,0 @@
-import { PluginContext } from 'molstar/lib/mol-plugin/context';
-import { JBrowsePluginProteinViewModel } from './model';
-export default function useProteinViewClickActionBehavior({ plugin, model, }: {
-    plugin?: PluginContext;
-    model: JBrowsePluginProteinViewModel;
-}): {
-    error: unknown;
-};

package/dist/ProteinView/useProteinViewClickBehavior.js

@@ -1,34 +0,0 @@
-import { useEffect, useState } from 'react';
-import { getSession } from '@jbrowse/core/util';
-import { clickProteinToGenome } from './proteinToGenomeMapping';
-import { StructureElement, StructureProperties as Props, } from 'molstar/lib/mol-model/structure';
-export default function useProteinViewClickActionBehavior({ plugin, model, }) {
-    const [error, setError] = useState();
-    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 };
-}
-//# sourceMappingURL=useProteinViewClickBehavior.js.map

package/dist/ProteinView/useProteinViewClickBehavior.js.map

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package/dist/ProteinView/useProteinViewHoverBehavior.d.ts

@@ -1,6 +0,0 @@
-import { PluginContext } from 'molstar/lib/mol-plugin/context';
-import { JBrowsePluginProteinViewModel } from './model';
-export default function useProteinViewClickActionBehavior({ plugin, model, }: {
-    plugin?: PluginContext;
-    model: JBrowsePluginProteinViewModel;
-}): void;

package/dist/ProteinView/useProteinViewHoverBehavior.js

@@ -1,31 +0,0 @@
-import { useEffect } from 'react';
-import { getSession } from '@jbrowse/core/util';
-import { StructureElement, StructureProperties as Props, } from 'molstar/lib/mol-model/structure';
-import { hoverProteinToGenome } from './proteinToGenomeMapping';
-export default function useProteinViewClickActionBehavior({ plugin, model, }) {
-    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]);
-}
-//# sourceMappingURL=useProteinViewHoverBehavior.js.map

package/dist/ProteinView/useProteinViewHoverBehavior.js.map

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