jbrowse-plugin-protein3d 0.6.0 → 0.8.0

package/dist/AddHighlightModel/GenomeTo1DProteinHoverHighlight.js

@@ -20,11 +20,14 @@ const GenomeTo1DProteinHoverHighlight = observer(function GenomeTo1DProteinHover
     if (!checkHovered(hovered)) {
         return null;
     }
-    const { coord } = hovered.hoverPosition;
+    const { coord, refName } = hovered.hoverPosition;
     const feature = new SimpleFeature(protein1DInfo.feature);
     const mapping = genomeToTranscriptSeqMapping(feature);
     const { g2p } = mapping;
-    const proteinPos = g2p[coord - 1];
+    // g2p is keyed by genomic position on the transcript's own refName; without
+    // this gate the same numeric coord on an unrelated chromosome would match a
+    // key and light a protein residue for a different locus.
+    const proteinPos = refName === mapping.refName ? g2p[coord - 1] : undefined;
     if (proteinPos === undefined) {
         return null;
     }

package/dist/AddHighlightModel/ProteinToMsaHoverSync.js

@@ -43,6 +43,10 @@ const ProteinToMsaHoverSync = observer(function ProteinToMsaHoverSync({ model, }
                         : seqPos;
                     setMousePos(col);
                 }
+                else {
+                    // structure went away (e.g. removed); clear the stale MSA hover
+                    setMousePos(undefined);
+                }
             }));
         }
         disposers.push(autorun(() => {

package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.d.ts

@@ -1,18 +1,18 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature, Region } from '@jbrowse/core/util';
-import type { Observable } from 'rxjs';
-export default class AlphaFoldConfidenceAdapter extends BaseFeatureDataAdapter {
-    static capabilities: string[];
-    feats: Promise<{
-        uniqueId: string;
-        start: number;
-        end: number;
-        score: number;
-    }[]> | undefined;
-    private loadDataP;
-    private loadData;
-    getRefNames(_opts?: BaseOptions): Promise<never[]>;
-    getFeatures(query: Region, _opts?: BaseOptions): Observable<Feature>;
-    freeResources(): void;
+import { BaseProteinAnnotationAdapter, type ProteinAnnotationRow } from '../BaseProteinAnnotationAdapter';
+export interface AlphaFoldConfidenceRow extends ProteinAnnotationRow {
+    score: number;
 }
+interface AlphaFoldConfidenceJson {
+    residueNumber: number[];
+    confidenceScore: number[];
+}
+/**
+ * Converts AlphaFold confidence JSON to features. residueNumber is 1-based, so
+ * residue n becomes the 0-based half-open interval [n-1, n) to line up with the
+ * interbase protein reference sequence.
+ */
+export declare function parseAlphaFoldConfidence(json: AlphaFoldConfidenceJson): AlphaFoldConfidenceRow[];
+export default class AlphaFoldConfidenceAdapter extends BaseProteinAnnotationAdapter<AlphaFoldConfidenceRow> {
+    protected loadFeatures(): Promise<AlphaFoldConfidenceRow[]>;
+}
+export {};

package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js

@@ -1,40 +1,21 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature, doesIntersect2 } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-export default class AlphaFoldConfidenceAdapter extends BaseFeatureDataAdapter {
-    static capabilities = ['getFeatures', 'getRefNames'];
-    feats;
-    async loadDataP() {
-        const scores = JSON.parse(await openLocation(this.getConf('location')).readFile('utf8'));
-        return scores.residueNumber.map((value, idx) => ({
-            uniqueId: `feat-${idx}`,
-            start: value,
-            end: value + 1,
-            score: scores.confidenceScore[idx],
-        }));
-    }
-    async loadData(_opts = {}) {
-        this.feats ??= this.loadDataP().catch((e) => {
-            this.feats = undefined;
-            throw e;
-        });
-        return this.feats;
-    }
-    async getRefNames(_opts = {}) {
-        return [];
-    }
-    getFeatures(query, _opts = {}) {
-        return ObservableCreate(async (observer) => {
-            const { start, end, refName } = query;
-            const data = await this.loadData();
-            for (const f of data) {
-                if (doesIntersect2(f.start, f.end, start, end)) {
-                    observer.next(new SimpleFeature({ ...f, refName }));
-                }
-            }
-            observer.complete();
-        });
+import { BaseProteinAnnotationAdapter, } from '../BaseProteinAnnotationAdapter';
+/**
+ * Converts AlphaFold confidence JSON to features. residueNumber is 1-based, so
+ * residue n becomes the 0-based half-open interval [n-1, n) to line up with the
+ * interbase protein reference sequence.
+ */
+export function parseAlphaFoldConfidence(json) {
+    return json.residueNumber.map((residue, idx) => ({
+        uniqueId: `feat-${idx}`,
+        start: residue - 1,
+        end: residue,
+        score: json.confidenceScore[idx],
+    }));
+}
+export default class AlphaFoldConfidenceAdapter extends BaseProteinAnnotationAdapter {
+    async loadFeatures() {
+        const json = JSON.parse(await openLocation(this.getConf('location')).readFile('utf8'));
+        return parseAlphaFoldConfidence(json);
     }
-    freeResources() { }
 }

package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.d.ts

@@ -1,28 +1,26 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseProteinAnnotationAdapter, type ProteinAnnotationRow } from '../BaseProteinAnnotationAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature, Region } from '@jbrowse/core/util';
-import type { Observable } from 'rxjs';
-export interface AlphaMissenseRow {
-    uniqueId: string;
-    start: number;
-    end: number;
+import type { Region } from '@jbrowse/core/util';
+export interface AlphaMissenseRow extends ProteinAnnotationRow {
     score: number;
     ref: string;
     variant: string;
     am_class: string;
 }
-/**
- * Parses AlphaMissense CSV text (protein_variant,score,am_class). The
- * protein_variant column looks like "V123L": a ref AA, a 1-based residue
- * coordinate, and a variant AA. Rows that don't parse to a numeric coordinate
- * are skipped rather than emitted as bogus position-0 features.
- */
 export declare function parseAlphaMissense(text: string): AlphaMissenseRow[];
-export default class AlphaMissensePathogenicityAdapter extends BaseFeatureDataAdapter {
-    static capabilities: string[];
-    feats: Promise<AlphaMissenseRow[]> | undefined;
-    private loadDataP;
-    private loadData;
+export default class AlphaMissensePathogenicityAdapter extends BaseProteinAnnotationAdapter<AlphaMissenseRow> {
+    protected loadFeatures(): Promise<AlphaMissenseRow[]>;
+    protected featureData(row: AlphaMissenseRow, refName: string): {
+        refName: string;
+        source: string;
+        score: number;
+        ref: string;
+        variant: string;
+        am_class: string;
+        uniqueId: string;
+        start: number;
+        end: number;
+    };
     getGlobalStats(_opts?: BaseOptions): Promise<{
         scoreMin: number;
         scoreMax: number;
@@ -30,11 +28,8 @@ export default class AlphaMissensePathogenicityAdapter extends BaseFeatureDataAd
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
-    getRefNames(_opts?: BaseOptions): Promise<never[]>;
-    getFeatures(query: Region, _opts?: BaseOptions): Observable<Feature>;
     getSources(): Promise<{
         name: string;
         __name: string;
     }[]>;
-    freeResources(): void;
 }

package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js

@@ -1,13 +1,15 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature, doesIntersect2, max, min } from '@jbrowse/core/util';
+import { max, min } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { BaseProteinAnnotationAdapter, } from '../BaseProteinAnnotationAdapter';
 /**
  * Parses AlphaMissense CSV text (protein_variant,score,am_class). The
  * protein_variant column looks like "V123L": a ref AA, a 1-based residue
- * coordinate, and a variant AA. Rows that don't parse to a numeric coordinate
- * are skipped rather than emitted as bogus position-0 features.
+ * coordinate, and a variant AA, converted here to a 0-based half-open interval
+ * to match the interbase protein reference sequence. Rows that don't match the
+ * ref/coord/variant shape are skipped rather than emitted as bogus features (a
+ * short string like "VL" would otherwise parse to a position-0 feature).
  */
+const VARIANT_RE = /^([A-Za-z])(\d+)([A-Za-z])$/;
 export function parseAlphaMissense(text) {
     return text
         .split('\n')
@@ -16,21 +18,15 @@ export function parseAlphaMissense(text) {
         .filter(f => !!f)
         .flatMap((row, idx) => {
         const [protein_variant = '', score, am_class] = row.split(',');
-        const ref = protein_variant[0];
-        const variant = protein_variant.at(-1);
-        const coord = +protein_variant.slice(1, -1);
-        return ref !== undefined &&
-            variant !== undefined &&
-            !Number.isNaN(coord) &&
-            score !== undefined &&
-            am_class !== undefined
+        const match = VARIANT_RE.exec(protein_variant);
+        return match && score !== undefined && am_class !== undefined
             ? [
                 {
                     uniqueId: `feat-${idx}`,
-                    ref,
-                    variant,
-                    start: coord,
-                    end: coord + 1,
+                    ref: match[1],
+                    variant: match[3],
+                    start: +match[2] - 1,
+                    end: +match[2],
                     score: +score,
                     am_class,
                 },
@@ -38,58 +34,23 @@ export function parseAlphaMissense(text) {
             : [];
     });
 }
-export default class AlphaMissensePathogenicityAdapter extends BaseFeatureDataAdapter {
-    static capabilities = ['getFeatures', 'getRefNames'];
-    feats;
-    async loadDataP() {
-        const scores = await openLocation(this.getConf('location')).readFile('utf8');
-        return parseAlphaMissense(scores);
+export default class AlphaMissensePathogenicityAdapter extends BaseProteinAnnotationAdapter {
+    async loadFeatures() {
+        return parseAlphaMissense(await openLocation(this.getConf('location')).readFile('utf8'));
     }
-    async loadData(_opts = {}) {
-        this.feats ??= this.loadDataP().catch((e) => {
-            this.feats = undefined;
-            throw e;
-        });
-        return this.feats;
+    featureData(row, refName) {
+        return { ...row, refName, source: row.variant };
     }
     async getGlobalStats(_opts) {
-        const data = await this.loadData();
-        const scores = data.map(s => s.score);
+        const scores = (await this.loadData()).map(s => s.score);
         return { scoreMin: min(scores), scoreMax: max(scores) };
     }
     // always render bigwig instead of calculating a feature density for it
     async getMultiRegionFeatureDensityStats(_regions) {
         return { featureDensity: 0 };
     }
-    async getRefNames(_opts = {}) {
-        return [];
-    }
-    getFeatures(query, _opts = {}) {
-        return ObservableCreate(async (observer) => {
-            const { start, end, refName } = query;
-            const data = await this.loadData();
-            for (const f of data) {
-                if (doesIntersect2(f.start, f.end, start, end)) {
-                    observer.next(new SimpleFeature({
-                        ...f,
-                        refName,
-                        source: f.variant,
-                    }));
-                }
-            }
-            observer.complete();
-        });
-    }
     async getSources() {
-        const sources = new Set();
-        const data = await this.loadData();
-        for (const f of data) {
-            sources.add(f.variant);
-        }
-        return [...sources].map(s => ({
-            name: s,
-            __name: s,
-        }));
+        const sources = new Set((await this.loadData()).map(f => f.variant));
+        return [...sources].map(s => ({ name: s, __name: s }));
     }
-    freeResources() { }
 }

package/dist/BaseProteinAnnotationAdapter.d.ts

@@ -0,0 +1,29 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region, SimpleFeatureSerialized } from '@jbrowse/core/util';
+import type { Observable } from 'rxjs';
+export interface ProteinAnnotationRow {
+    [key: string]: unknown;
+    uniqueId: string;
+    start: number;
+    end: number;
+}
+/**
+ * Shared plumbing for the protein-annotation adapters (AlphaFold confidence,
+ * AlphaMissense, UniProt variation). Each lives on the temporary protein
+ * assembly, exposes no ref names, caches its parsed rows once, and emits the
+ * rows that intersect a query region. Subclasses supply the parsing
+ * (loadFeatures) and may decorate the emitted feature (featureData).
+ */
+export declare abstract class BaseProteinAnnotationAdapter<T extends ProteinAnnotationRow> extends BaseFeatureDataAdapter {
+    static capabilities: string[];
+    private feats;
+    /** Parse the configured source into rows. */
+    protected abstract loadFeatures(): Promise<T[]>;
+    /** Fields for the emitted feature; override to add extras (e.g. `source`). */
+    protected featureData(row: T, refName: string): SimpleFeatureSerialized;
+    protected loadData(): Promise<T[]>;
+    getRefNames(_opts?: BaseOptions): Promise<never[]>;
+    getFeatures(query: Region, _opts?: BaseOptions): Observable<Feature>;
+    freeResources(): void;
+}

package/dist/BaseProteinAnnotationAdapter.js

@@ -0,0 +1,41 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, doesIntersect2 } from '@jbrowse/core/util';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+/**
+ * Shared plumbing for the protein-annotation adapters (AlphaFold confidence,
+ * AlphaMissense, UniProt variation). Each lives on the temporary protein
+ * assembly, exposes no ref names, caches its parsed rows once, and emits the
+ * rows that intersect a query region. Subclasses supply the parsing
+ * (loadFeatures) and may decorate the emitted feature (featureData).
+ */
+export class BaseProteinAnnotationAdapter extends BaseFeatureDataAdapter {
+    static capabilities = ['getFeatures', 'getRefNames'];
+    feats;
+    /** Fields for the emitted feature; override to add extras (e.g. `source`). */
+    featureData(row, refName) {
+        return { ...row, refName };
+    }
+    // Parse once and cache; a failed parse clears the cache so it can retry.
+    loadData() {
+        this.feats ??= this.loadFeatures().catch((e) => {
+            this.feats = undefined;
+            throw e;
+        });
+        return this.feats;
+    }
+    async getRefNames(_opts = {}) {
+        return [];
+    }
+    getFeatures(query, _opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { start, end, refName } = query;
+            for (const f of await this.loadData()) {
+                if (doesIntersect2(f.start, f.end, start, end)) {
+                    observer.next(new SimpleFeature(this.featureData(f, refName)));
+                }
+            }
+            observer.complete();
+        });
+    }
+    freeResources() { }
+}

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/components/FoldseekSearch.js

@@ -36,9 +36,19 @@ const FoldseekSearch = observer(function FoldseekSearch({ feature, session, view
         ? stripStopCodon(selectedIsoformData.seq)
         : '';
     const sequence = userEditedSequence ?? cleanedSequence;
+    // Any change to the input sequence makes an existing 3Di prediction (and any
+    // results derived from it) stale. Clearing it returns the UI to the Predict
+    // step so a search can't silently run against the previously-predicted
+    // sequence after the user switches transcript or edits the residues.
+    const invalidatePrediction = () => {
+        if (di3Sequence !== undefined || results !== undefined) {
+            reset();
+        }
+    };
     const setUserSelectionWithReset = (id) => {
         setUserSelection(id);
         setUserEditedSequence(undefined);
+        invalidatePrediction();
     };
     const canPredict = sequence.trim().length > 0 && !isPredicting && !isLoading;
     const canSearch = !!cleanedAaSequence &&
@@ -55,6 +65,7 @@ const FoldseekSearch = observer(function FoldseekSearch({ feature, session, view
                 React.createElement(TranscriptSelector, { val: effectiveSelectedTranscriptId, setVal: setUserSelectionWithReset, isoforms: transcripts, isoformSequences: isoformSequences, feature: feature, disabled: isBusy }),
                 React.createElement(TextField, { label: "Protein sequence (amino acids)", multiline: true, rows: 4, value: sequence, onChange: e => {
                         setUserEditedSequence(e.target.value);
+                        invalidatePrediction();
                     }, placeholder: `MKTVRQERLKSIVRILERSKEPVSGAQLAEEL...`, disabled: isBusy, InputProps: {
                         className: classes.sequenceInput,
                     } }))) : null,

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;
@@ -24,11 +24,14 @@ export default function useUniProtSearch({ recognizedIds = [], geneId, geneName,
             selectedQueryId,
             idsToSearch.join(','),
             geneNameToSearch,
+            geneId,
+            organismId,
         ]
         : null, async () => searchUniProtEntries({
         recognizedIds: idsToSearch,
         geneId,
         geneName: geneNameToSearch,
+        organismId,
     }), {
         ...STATIC_SWR_OPTIONS,
         keepPreviousData: true,

package/dist/LaunchProteinView/services/lookupMethods.js

@@ -53,7 +53,7 @@ export async function searchUniProtEntries({ recognizedIds = [], geneId, geneNam
     let geneNameError;
     if (!entries.some(e => e.isReviewed) && geneName) {
         try {
-            const query = `gene:${geneName}+AND+organism_id:${organismId}+AND+reviewed:true`;
+            const query = `gene:${geneName} AND organism_id:${organismId} AND reviewed:true`;
             const geneNameResults = await searchUniProt(query, 5);
             entries = deduplicateEntries([...entries, ...geneNameResults]);
         }

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 {};