jbrowse-plugin-protein3d 0.7.0 → 0.8.0

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js

@@ -1,6 +1,6 @@
 import React from 'react';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
-import { DialogActions, DialogContent, Typography } from '@mui/material';
+import { DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import AlphaFoldDBSearchStatus from './AlphaFoldDBSearchStatus';
@@ -28,6 +28,12 @@ const useStyles = makeStyles()({
         gap: 20,
         alignItems: 'flex-start',
     },
+    endRow: {
+        display: 'flex',
+        flexDirection: 'row',
+        gap: 12,
+        alignItems: 'flex-start',
+    },
 });
 const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, session, view, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }) {
     const { classes } = useStyles();
@@ -35,7 +41,9 @@ const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, session
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             state.error ? React.createElement(ErrorMessage, { error: state.error }) : null,
-            React.createElement(UniProtIdInput, { lookupMode: state.lookupMode, onLookupModeChange: state.setLookupMode, manualUniprotId: state.manualUniprotId, onManualUniprotIdChange: state.setManualUniprotId, featureUniprotId: state.featureUniprotId, hasProteinSequence: !!state.userSelectedProteinSequence?.seq, sequenceSearchType: state.sequenceSearchType, onSequenceSearchTypeChange: state.setSequenceSearchType, endContent: state.showIdentifierSelector ? (React.createElement(IdentifierSelector, { recognizedIds: state.recognizedIds, geneName: state.geneName, selectedId: state.selectedQueryId, onSelectedIdChange: state.setSelectedQueryId })) : null }),
+            React.createElement(UniProtIdInput, { lookupMode: state.lookupMode, onLookupModeChange: state.setLookupMode, manualUniprotId: state.manualUniprotId, onManualUniprotIdChange: state.setManualUniprotId, featureUniprotId: state.featureUniprotId, hasProteinSequence: !!state.userSelectedProteinSequence?.seq, sequenceSearchType: state.sequenceSearchType, onSequenceSearchTypeChange: state.setSequenceSearchType, endContent: state.showIdentifierSelector ? (React.createElement("div", { className: classes.endRow },
+                    React.createElement(IdentifierSelector, { recognizedIds: state.recognizedIds, geneName: state.geneName, selectedId: state.selectedQueryId, onSelectedIdChange: state.setSelectedQueryId }),
+                    React.createElement(TextField, { size: "small", label: "Organism (NCBI taxon)", helperText: "Scopes the gene-name search", value: state.taxonId, onChange: event => { state.setTaxonId(event.target.value); }, placeholder: String(state.effectiveTaxonId), slotProps: { inputLabel: { shrink: true } }, sx: { width: 180 } }))) : null }),
             state.loadingStatuses.map(status => (React.createElement(LoadingEllipses, { key: status, variant: "subtitle2", message: status }))),
             state.showUniprotResults && (React.createElement(React.Fragment, null,
                 React.createElement(Typography, { variant: "body2", color: "textSecondary" },

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.d.ts

@@ -10,6 +10,9 @@ export default function useAlphaFoldDBSearch({ feature, view, }: {
     setLookupMode: import("react").Dispatch<import("react").SetStateAction<LookupMode>>;
     manualUniprotId: string;
     setManualUniprotId: import("react").Dispatch<import("react").SetStateAction<string>>;
+    taxonId: string;
+    setTaxonId: import("react").Dispatch<import("react").SetStateAction<string>>;
+    effectiveTaxonId: number;
     selectedQueryId: string;
     setSelectedQueryId: import("react").Dispatch<import("react").SetStateAction<string>>;
     sequenceSearchType: SequenceSearchType;

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.js

@@ -1,15 +1,34 @@
 import { useState } from 'react';
+import { getConf } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
 import useAlphaFoldData from './useAlphaFoldData';
 import useAlphaFoldSequenceSearch from './useAlphaFoldSequenceSearch';
 import useDebouncedValue from './useDebouncedValue';
 import useTranscriptIsoformSelection from './useTranscriptIsoformSelection';
 import useUniProtSearch from './useUniProtSearch';
 import getSearchDescription from '../utils/getSearchDescription';
-import { extractFeatureIdentifiers, stripStopCodon } from '../utils/util';
+import { extractFeatureIdentifiers, extractTaxonId, stripStopCodon, } from '../utils/util';
 export default function useAlphaFoldDBSearch({ feature, view, }) {
     const [lookupMode, setLookupMode] = useState('auto');
     const [manualUniprotId, setManualUniprotId] = useState('');
+    const [taxonIdInput, setTaxonIdInput] = useState('');
     const geneIds = extractFeatureIdentifiers(feature);
+    // The gene-name UniProt search is ambiguous across species, so scope it to
+    // the assembly's organism. jb2hubs assemblies carry the NCBI taxon in the
+    // reference-sequence track metadata (UCSC: metadata.taxId, GenArk:
+    // metadata.ucsc.taxId). Falls back to human via searchUniProtEntries when
+    // absent; a user override (taxonIdInput) always wins.
+    const assemblyName = view.assemblyNames[0];
+    const assembly = assemblyName
+        ? getSession(view).assemblyManager.get(assemblyName)
+        : undefined;
+    const assemblyTaxonId = assembly
+        ? extractTaxonId(getConf(assembly, ['sequence', 'metadata']))
+        : undefined;
+    const overrideTaxon = Number(taxonIdInput.trim());
+    const effectiveTaxonId = taxonIdInput.trim() !== '' && Number.isFinite(overrideTaxon) && overrideTaxon > 0
+        ? overrideTaxon
+        : assemblyTaxonId;
     const [selectedQueryId, setSelectedQueryId] = useState('auto');
     const [sequenceSearchType, setSequenceSearchType] = useState('md5');
     const [selectedUniprotId, setSelectedUniprotId] = useState();
@@ -21,6 +40,7 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         recognizedIds: geneIds.recognizedIds,
         geneId: geneIds.geneId,
         geneName: geneIds.geneName,
+        organismId: effectiveTaxonId,
         selectedQueryId,
         enabled: isAutoMode,
     });
@@ -84,6 +104,10 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         setLookupMode,
         manualUniprotId,
         setManualUniprotId,
+        taxonId: taxonIdInput,
+        setTaxonId: setTaxonIdInput,
+        // shown as the field placeholder so the user sees the organism in effect
+        effectiveTaxonId: effectiveTaxonId ?? 9606,
         selectedQueryId,
         setSelectedQueryId,
         sequenceSearchType,

package/dist/LaunchProteinView/hooks/useUniProtSearch.d.ts

@@ -1,8 +1,9 @@
 import type { UniProtEntry } from '../services/lookupMethods';
-export default function useUniProtSearch({ recognizedIds, geneId, geneName, selectedQueryId, enabled, }: {
+export default function useUniProtSearch({ recognizedIds, geneId, geneName, organismId, selectedQueryId, enabled, }: {
     recognizedIds?: string[];
     geneId?: string;
     geneName?: string;
+    organismId?: number;
     selectedQueryId?: string;
     enabled?: boolean;
 }): {

package/dist/LaunchProteinView/hooks/useUniProtSearch.js

@@ -2,7 +2,7 @@ import useSWR from 'swr';
 import { STATIC_SWR_OPTIONS } from './swrOptions';
 import { searchUniProtEntries } from '../services/lookupMethods';
 import { isRecognizedDatabaseId } from '../utils/util';
-export default function useUniProtSearch({ recognizedIds = [], geneId, geneName, selectedQueryId = 'auto', enabled = true, }) {
+export default function useUniProtSearch({ recognizedIds = [], geneId, geneName, organismId, selectedQueryId = 'auto', enabled = true, }) {
     // Determine what to search based on selectedQueryId
     let idsToSearch = [];
     let geneNameToSearch;
@@ -25,11 +25,13 @@ export default function useUniProtSearch({ recognizedIds = [], geneId, geneName,
             idsToSearch.join(','),
             geneNameToSearch,
             geneId,
+            organismId,
         ]
         : null, async () => searchUniProtEntries({
         recognizedIds: idsToSearch,
         geneId,
         geneName: geneNameToSearch,
+        organismId,
     }), {
         ...STATIC_SWR_OPTIONS,
         keepPreviousData: true,

package/dist/LaunchProteinView/utils/launchViewUtils.d.ts

@@ -1,3 +1,5 @@
+import { ALPHAFOLD_VERSION, getAlphaFoldConfidenceUrl, getAlphaFoldMsaUrl, getAlphaFoldStructureUrl, getConfidenceUrlFromTarget, getPdbStructureUrl, getStructureUrlFromTarget, getUniprotIdFromAlphaFoldTarget } from './structureUrls';
+export { ALPHAFOLD_VERSION, getAlphaFoldConfidenceUrl, getAlphaFoldMsaUrl, getAlphaFoldStructureUrl, getConfidenceUrlFromTarget, getPdbStructureUrl, getStructureUrlFromTarget, getUniprotIdFromAlphaFoldTarget, };
 import type { AbstractSessionModel, Feature, SessionWithAddTracks } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 declare global {
@@ -5,14 +7,6 @@ declare global {
         JBrowsePluginMsaView?: unknown;
     }
 }
-export declare const ALPHAFOLD_VERSION = "v6";
-export declare function getAlphaFoldStructureUrl(uniprotId: string, version?: string): string;
-export declare function getAlphaFoldConfidenceUrl(uniprotId: string, version?: string): string;
-export declare function getAlphaFoldMsaUrl(uniprotId: string, version?: string): string;
-export declare function getPdbStructureUrl(pdbId: string): string;
-export declare function getUniprotIdFromAlphaFoldTarget(target: string): string | undefined;
-export declare function getStructureUrlFromTarget(target: string, db: string): string | undefined;
-export declare function getConfidenceUrlFromTarget(target: string): string | undefined;
 interface LaunchViewParams {
     session: AbstractSessionModel;
     view: LinearGenomeViewModel;
@@ -48,4 +42,3 @@ export declare function getConditionalProteinLaunches({ session, view, feature,
     launchMsa: (() => import("@jbrowse/core/util").AbstractViewModel | undefined) | undefined;
 };
 export declare function launch3DProteinViewWithMsa(params: LaunchViewParams & Launch3DExtraParams): import("@jbrowse/core/util").AbstractViewModel | undefined;
-export {};

package/dist/LaunchProteinView/utils/launchViewUtils.js

@@ -1,53 +1,11 @@
 import { isSessionWithAddTracks } from '@jbrowse/core/util';
 import { maybeLaunchSideBySide } from './sideBySide';
+import { ALPHAFOLD_VERSION, getAlphaFoldConfidenceUrl, getAlphaFoldMsaUrl, getAlphaFoldStructureUrl, getConfidenceUrlFromTarget, getPdbStructureUrl, getStructureUrlFromTarget, getUniprotIdFromAlphaFoldTarget, } from './structureUrls';
 import { getGeneDisplayName, getTranscriptDisplayName } from './util';
 import { proteinViewSnapshot } from '../../ProteinView/proteinViewSpec';
 import { launchProteinAnnotationView } from '../components/launchProteinAnnotationView';
-export const ALPHAFOLD_VERSION = 'v6';
-export function getAlphaFoldStructureUrl(uniprotId, version = ALPHAFOLD_VERSION) {
-    return `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-model_${version}.cif`;
-}
-export function getAlphaFoldConfidenceUrl(uniprotId, version = ALPHAFOLD_VERSION) {
-    return `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-confidence_${version}.json`;
-}
-export function getAlphaFoldMsaUrl(uniprotId, version = ALPHAFOLD_VERSION) {
-    return `https://alphafold.ebi.ac.uk/files/msa/AF-${uniprotId}-F1-msa_${version}.a3m`;
-}
-export function getPdbStructureUrl(pdbId) {
-    return `https://files.rcsb.org/download/${pdbId}.cif`;
-}
-// Foldseek targets may contain a description after the ID separated by a
-// space, e.g. "AF-P16442-F1-model_v6 Histo-blood group ABO transferase".
-function extractTargetId(target) {
-    return target.split(' ')[0];
-}
-export function getUniprotIdFromAlphaFoldTarget(target) {
-    // Handles both "AF-P16442-F1-model_v6" and full URLs like
-    // "https://alphafold.ebi.ac.uk/files/AF-P16442-F1-model_v6.cif"
-    const match = /AF-([A-Z0-9]+)-F\d+/.exec(extractTargetId(target));
-    return match?.[1];
-}
-export function getStructureUrlFromTarget(target, db) {
-    const targetId = extractTargetId(target);
-    if (targetId.startsWith('AF-')) {
-        return `https://alphafold.ebi.ac.uk/files/${targetId}.cif`;
-    }
-    if (db === 'pdb100') {
-        const pdbId = targetId.split('_')[0];
-        if (pdbId.length === 4) {
-            return getPdbStructureUrl(pdbId);
-        }
-    }
-    return undefined;
-}
-export function getConfidenceUrlFromTarget(target) {
-    const targetId = extractTargetId(target);
-    if (targetId.startsWith('AF-')) {
-        const confidenceId = targetId.replace('-model_', '-confidence_');
-        return `https://alphafold.ebi.ac.uk/files/${confidenceId}.json`;
-    }
-    return undefined;
-}
+// Re-exported so existing importers keep their `launchViewUtils` import path.
+export { ALPHAFOLD_VERSION, getAlphaFoldConfidenceUrl, getAlphaFoldMsaUrl, getAlphaFoldStructureUrl, getConfidenceUrlFromTarget, getPdbStructureUrl, getStructureUrlFromTarget, getUniprotIdFromAlphaFoldTarget, };
 export function formatViewName(prefix, feature, selectedTranscript, uniprotId) {
     return [
         ...new Set([

package/dist/LaunchProteinView/utils/structureUrls.d.ts

@@ -0,0 +1,8 @@
+export declare const ALPHAFOLD_VERSION = "v6";
+export declare function getAlphaFoldStructureUrl(uniprotId: string, version?: string): string;
+export declare function getAlphaFoldConfidenceUrl(uniprotId: string, version?: string): string;
+export declare function getAlphaFoldMsaUrl(uniprotId: string, version?: string): string;
+export declare function getPdbStructureUrl(pdbId: string): string;
+export declare function getUniprotIdFromAlphaFoldTarget(target: string): string | undefined;
+export declare function getStructureUrlFromTarget(target: string, db: string): string | undefined;
+export declare function getConfidenceUrlFromTarget(target: string): string | undefined;

package/dist/LaunchProteinView/utils/structureUrls.js

@@ -0,0 +1,48 @@
+// Pure structure-URL builders and target parsers. Kept dependency-free so both
+// the launch flow and the ProteinView model (e.g. resolving a `uniprotId`/`pdbId`
+// shorthand at hydration) can import them without pulling in heavy launch code.
+export const ALPHAFOLD_VERSION = 'v6';
+export function getAlphaFoldStructureUrl(uniprotId, version = ALPHAFOLD_VERSION) {
+    return `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-model_${version}.cif`;
+}
+export function getAlphaFoldConfidenceUrl(uniprotId, version = ALPHAFOLD_VERSION) {
+    return `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-confidence_${version}.json`;
+}
+export function getAlphaFoldMsaUrl(uniprotId, version = ALPHAFOLD_VERSION) {
+    return `https://alphafold.ebi.ac.uk/files/msa/AF-${uniprotId}-F1-msa_${version}.a3m`;
+}
+export function getPdbStructureUrl(pdbId) {
+    return `https://files.rcsb.org/download/${pdbId}.cif`;
+}
+// Foldseek targets may contain a description after the ID separated by a
+// space, e.g. "AF-P16442-F1-model_v6 Histo-blood group ABO transferase".
+function extractTargetId(target) {
+    return target.split(' ')[0];
+}
+export function getUniprotIdFromAlphaFoldTarget(target) {
+    // Handles both "AF-P16442-F1-model_v6" and full URLs like
+    // "https://alphafold.ebi.ac.uk/files/AF-P16442-F1-model_v6.cif"
+    const match = /AF-([A-Z0-9]+)-F\d+/.exec(extractTargetId(target));
+    return match?.[1];
+}
+export function getStructureUrlFromTarget(target, db) {
+    const targetId = extractTargetId(target);
+    if (targetId.startsWith('AF-')) {
+        return `https://alphafold.ebi.ac.uk/files/${targetId}.cif`;
+    }
+    if (db === 'pdb100') {
+        const pdbId = targetId.split('_')[0];
+        if (pdbId.length === 4) {
+            return getPdbStructureUrl(pdbId);
+        }
+    }
+    return undefined;
+}
+export function getConfidenceUrlFromTarget(target) {
+    const targetId = extractTargetId(target);
+    if (targetId.startsWith('AF-')) {
+        const confidenceId = targetId.replace('-model_', '-confidence_');
+        return `https://alphafold.ebi.ac.uk/files/${confidenceId}.json`;
+    }
+    return undefined;
+}

package/dist/LaunchProteinView/utils/util.d.ts

@@ -1,5 +1,13 @@
 import type { Feature } from '@jbrowse/core/util';
 export declare function stripStopCodon(seq: string): string;
+/**
+ * Pull an NCBI taxon id out of reference-sequence-track metadata. jb2hubs
+ * assemblies expose it differently by source: UCSC golden-path spreads it flat
+ * (`metadata.taxId`), GenArk nests the raw hub stanza (`metadata.ucsc.taxId`).
+ * `taxonId` is accepted too. Returns a positive integer, or undefined when
+ * absent/unparseable so callers can fall back to a default organism.
+ */
+export declare function extractTaxonId(metadata: unknown): number | undefined;
 export declare function getTranscriptFeatures(feature: Feature): Feature[];
 export declare function stripTrailingVersion(s?: string): string | undefined;
 export declare function getId(val?: Feature): string;

package/dist/LaunchProteinView/utils/util.js

@@ -1,6 +1,24 @@
 export function stripStopCodon(seq) {
     return seq.replaceAll('*', '');
 }
+/**
+ * Pull an NCBI taxon id out of reference-sequence-track metadata. jb2hubs
+ * assemblies expose it differently by source: UCSC golden-path spreads it flat
+ * (`metadata.taxId`), GenArk nests the raw hub stanza (`metadata.ucsc.taxId`).
+ * `taxonId` is accepted too. Returns a positive integer, or undefined when
+ * absent/unparseable so callers can fall back to a default organism.
+ */
+export function extractTaxonId(metadata) {
+    if (metadata === null || typeof metadata !== 'object') {
+        return undefined;
+    }
+    const m = metadata;
+    const ucsc = m.ucsc !== null && typeof m.ucsc === 'object'
+        ? m.ucsc
+        : undefined;
+    const n = Number(m.taxId ?? m.taxonId ?? ucsc?.taxId);
+    return Number.isFinite(n) && n > 0 ? n : undefined;
+}
 export function getTranscriptFeatures(feature) {
     // 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

package/dist/ProteinView/proteinViewSpec.d.ts

@@ -9,6 +9,8 @@ import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export interface ProteinStructureSpec {
     url?: string;
     data?: string;
+    uniprotId?: string;
+    pdbId?: string;
     connectedViewId?: string;
     feature?: SimpleFeatureSerialized;
     userProvidedTranscriptSequence?: string;
@@ -48,6 +50,8 @@ export declare function proteinViewSnapshot(spec: ProteinViewSpec): {
         userProvidedTranscriptSequence: string;
         url?: string;
         data?: string;
+        uniprotId?: string;
+        pdbId?: string;
         connectedViewId?: string;
         feature?: SimpleFeatureSerialized;
         initialSelection?: {

package/dist/ProteinView/structureModel.js

@@ -12,7 +12,7 @@ import { kyteDoolittleScores, mapResidueValuesToColumns } from './residueTracks'
 import subscribeMolstarInteraction from './subscribeMolstarInteraction';
 import { coerceAlignmentAlgorithm } from './types';
 import { checkHovered } from './util';
-import { getUniprotIdFromAlphaFoldTarget } from '../LaunchProteinView/utils/launchViewUtils';
+import { getAlphaFoldStructureUrl, getPdbStructureUrl, getUniprotIdFromAlphaFoldTarget, } from '../LaunchProteinView/utils/structureUrls';
 import { stripStopCodon } from '../LaunchProteinView/utils/util';
 import { genomeToTranscriptSeqMapping } from '../mappings';
 const Structure = types
@@ -52,6 +52,24 @@ const Structure = types
      * session spec open with a domain pre-highlighted, with no click.
      */
     initialSelection: types.frozen(),
+})
+    // Input-only shorthand: remap a `{ uniprotId }`/`{ pdbId }` snapshot to a
+    // concrete `url` at hydration and strip the shorthand keys (they are not
+    // stored — uniprotId stays derivable from the url via the getter below), so a
+    // hand-authored snapshot loads without the caller knowing the AlphaFold/RCSB
+    // URL format. An explicit url/data always wins; the shorthand resolves the
+    // canonical isoform (AF-<id>-F1) only. Idempotent: a re-snapshot has no
+    // shorthand keys and an already-set url, so it passes through unchanged.
+    .preProcessSnapshot(({ uniprotId, pdbId, ...rest }) => {
+    const hasSource = rest.url !== undefined || rest.data !== undefined;
+    const url = hasSource
+        ? rest.url
+        : uniprotId !== undefined
+            ? getAlphaFoldStructureUrl(uniprotId)
+            : pdbId !== undefined
+                ? getPdbStructureUrl(pdbId)
+                : rest.url;
+    return { ...rest, url };
 })
     .volatile(() => ({
     /**