jbrowse-plugin-protein3d 0.4.5 → 0.4.6

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js

@@ -5,7 +5,6 @@ import { DialogActions, DialogContent, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import AlphaFoldDBSearchStatus from './AlphaFoldDBSearchStatus';
-import AlphaFoldEntrySelector from './AlphaFoldEntrySelector';
 import IdentifierSelector from './IdentifierSelector';
 import ProteinViewActions from './ProteinViewActions';
 import SequenceSearchStatus from './SequenceSearchStatus';
@@ -62,8 +61,7 @@ const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, model,
                 "directly and use \"Enter manually\" above, or use \"Search sequence against AlphaFoldDB API\" if available.")),
             state.showStructureSelectors && (React.createElement(React.Fragment, null,
                 React.createElement("div", { className: classes.selectorsRow },
-                    React.createElement(TranscriptSelector, { val: state.userSelection, setVal: state.setUserSelection, structureSequence: state.structureSequence, feature: feature, isoforms: state.transcriptOptions, isoformSequences: state.isoformSequences }),
-                    state.showAlphaFoldEntrySelector && (React.createElement(AlphaFoldEntrySelector, { predictions: state.predictions, selectedEntryIndex: state.selectedEntryIndex, onSelectionChange: state.setSelectedEntryIndex }))),
+                    React.createElement(TranscriptSelector, { val: state.userSelection, setVal: state.setUserSelection, structureSequence: state.structureSequence, feature: feature, isoforms: state.transcriptOptions, isoformSequences: state.isoformSequences })),
                 state.showSequenceSearchStatus && (React.createElement(SequenceSearchStatus, { isLoading: state.isSequenceSearchLoading, uniprotId: state.uniprotId, url: state.url, hasProteinSequence: !!state.userSelectedProteinSequence, sequenceSearchType: state.sequenceSearchType })),
                 state.showAlphaFoldDBSearchStatus && (React.createElement(AlphaFoldDBSearchStatus, { uniprotId: state.uniprotId, selectedTranscript: state.selectedTranscript, structureSequence: state.structureSequence, isoformSequences: state.isoformSequences, url: state.url }))))),
         React.createElement(DialogActions, null,

package/dist/LaunchProteinView/components/FoldseekSearch.js

@@ -76,8 +76,12 @@ const FoldseekSearch = observer(function FoldseekSearch({ feature, model, handle
             statusMessage ? (React.createElement(LoadingEllipses, { variant: "subtitle2", message: statusMessage })) : null,
             results ? (React.createElement(FoldseekResultsTable, { results: results, session: session, view: view, feature: feature, selectedTranscript: selectedTranscript, userProvidedTranscriptSequence: sequence, onClose: handleClose })) : null),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel"),
-            results ? (React.createElement(Button, { variant: "outlined", onClick: reset }, "New search")) : null,
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
+            results ? (React.createElement(Button, { variant: "outlined", onClick: () => {
+                    reset();
+                } }, "New search")) : null,
             !di3Sequence ? (React.createElement(Button, { variant: "contained", color: "primary", disabled: !canPredict, onClick: () => {
                     if (sequence.trim()) {
                         void predictStructure(sequence.trim());

package/dist/LaunchProteinView/components/IdentifierSelector.d.ts

@@ -1,10 +1,9 @@
 import React from 'react';
 interface IdentifierSelectorProps {
     recognizedIds: string[];
-    uniprotId?: string;
     geneName?: string;
     selectedId: string;
     onSelectedIdChange: (id: string) => void;
 }
-export default function IdentifierSelector({ recognizedIds, uniprotId, geneName, selectedId, onSelectedIdChange, }: IdentifierSelectorProps): React.JSX.Element | null;
+export default function IdentifierSelector({ recognizedIds, geneName, selectedId, onSelectedIdChange, }: IdentifierSelectorProps): React.JSX.Element | null;
 export {};

package/dist/LaunchProteinView/components/IdentifierSelector.js

@@ -35,26 +35,20 @@ function getIdLabel(id) {
     }
     return id;
 }
-export default function IdentifierSelector({ recognizedIds, uniprotId, geneName, selectedId, onSelectedIdChange, }) {
+export default function IdentifierSelector({ recognizedIds, geneName, selectedId, onSelectedIdChange, }) {
     const [expanded, setExpanded] = useState(false);
     // Build list of selectable options
     const options = [
         { value: 'auto', label: 'Auto (try all)' },
         ...recognizedIds.map(id => ({ value: id, label: getIdLabel(id) })),
     ];
-    if (uniprotId) {
-        options.push({
-            value: `uniprot:${uniprotId}`,
-            label: `${uniprotId} (UniProt)`,
-        });
-    }
     if (geneName) {
         options.push({
             value: `gene:${geneName}`,
             label: `${geneName} (gene name)`,
         });
     }
-    if (recognizedIds.length === 0 && !uniprotId && !geneName) {
+    if (recognizedIds.length === 0 && !geneName) {
         return null;
     }
     if (!expanded) {

package/dist/LaunchProteinView/components/UserProvidedStructure.js

@@ -40,16 +40,18 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
     const [submitError, setSubmitError] = useState();
     const [structureURL, setStructureURL] = useState('');
     const [showAllProteinSequences, setShowAllProteinSequences] = useState(false);
+    const activeFile = choice === 'file' ? file : undefined;
+    const activeURL = choice === 'file' ? '' : structureURL;
     const options = getTranscriptFeatures(feature);
     const view = getContainingView(model);
     const { isoformSequences, error: isoformError } = useIsoformProteinSequences({
         feature,
         view,
     });
-    const { sequences: structureSequences1, error: localFileError } = useLocalStructureFileSequence({ file });
-    const { sequences: structureSequences2, error: remoteFileError } = useRemoteStructureFileSequence({ url: structureURL });
-    const structureName = file?.name ?? structureURL.slice(structureURL.lastIndexOf('/') + 1);
-    const structureSequences = structureSequences1 ?? structureSequences2;
+    const { sequences: localSequences, error: localFileError } = useLocalStructureFileSequence({ file: activeFile });
+    const { sequences: remoteSequences, error: remoteFileError } = useRemoteStructureFileSequence({ url: activeURL });
+    const structureName = activeFile?.name ?? activeURL.slice(activeURL.lastIndexOf('/') + 1);
+    const structureSequences = activeFile ? localSequences : remoteSequences;
     const structureSequence = structureSequences?.[0];
     const { userSelection, setUserSelection } = useTranscriptSelection({
         options,
@@ -59,7 +61,7 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
     const selectedTranscript = options.find(val => getId(val) === userSelection);
     const protein = userSelection ? isoformSequences?.[userSelection] : undefined;
     const error = isoformError ?? submitError ?? localFileError ?? remoteFileError;
-    const canLaunch = !!(structureURL || file) && !!protein && !!selectedTranscript;
+    const canLaunch = !!(activeURL || activeFile) && !!protein && !!selectedTranscript;
     const sequencesDiffer = !!protein?.seq &&
         !!structureSequence &&
         stripStopCodon(protein.seq) !== structureSequence;
@@ -68,8 +70,8 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
             return;
         }
         try {
-            const structureData = file ? await file.text() : undefined;
-            const url = structureURL ? structureURL : undefined;
+            const structureData = activeFile ? await activeFile.text() : undefined;
+            const url = activeURL ? activeURL : undefined;
             if (!url && !structureData) {
                 return;
             }

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

@@ -15,7 +15,7 @@ export default function useAlphaFoldDBSearch({ feature, view, }: {
     sequenceSearchType: SequenceSearchType;
     setSequenceSearchType: import("react").Dispatch<import("react").SetStateAction<SequenceSearchType>>;
     selectedUniprotId: string | undefined;
-    setSelectedUniprotId: (id: string | undefined) => void;
+    setSelectedUniprotId: import("react").Dispatch<import("react").SetStateAction<string | undefined>>;
     userSelection: string | undefined;
     setUserSelection: import("react").Dispatch<import("react").SetStateAction<string | undefined>>;
     transcriptOptions: Feature[];
@@ -29,9 +29,6 @@ export default function useAlphaFoldDBSearch({ feature, view, }: {
         seq: string;
     } | undefined;
     uniprotEntries: import("../services/lookupMethods").UniProtEntry[];
-    predictions: import("./useAlphaFoldUrl").AlphaFoldPrediction[] | undefined;
-    selectedEntryIndex: number;
-    setSelectedEntryIndex: import("react").Dispatch<import("react").SetStateAction<number>>;
     recognizedIds: string[];
     geneName: string | undefined;
     featureUniprotId: string | undefined;
@@ -50,7 +47,6 @@ export default function useAlphaFoldDBSearch({ feature, view, }: {
     selectedTableAccession: string | undefined;
     showUniprotResults: boolean;
     showNoResults: boolean;
-    showAlphaFoldEntrySelector: boolean;
     showSequenceSearchStatus: boolean;
     showAlphaFoldDBSearchStatus: boolean;
     isLoading: boolean;

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.js

@@ -3,9 +3,10 @@ import useAlphaFoldData from './useAlphaFoldData';
 import useAlphaFoldSequenceSearch from './useAlphaFoldSequenceSearch';
 import useDebouncedValue from './useDebouncedValue';
 import useIsoformProteinSequences from './useIsoformProteinSequences';
+import useTranscriptSelection from './useTranscriptSelection';
 import useUniProtSearch from './useUniProtSearch';
 import getSearchDescription from '../utils/getSearchDescription';
-import { extractFeatureIdentifiers, getId, getTranscriptFeatures, selectBestTranscript, stripStopCodon, } from '../utils/util';
+import { extractFeatureIdentifiers, getId, getTranscriptFeatures, stripStopCodon, } from '../utils/util';
 export default function useAlphaFoldDBSearch({ feature, view, }) {
     const [lookupMode, setLookupMode] = useState('auto');
     const [manualUniprotId, setManualUniprotId] = useState('');
@@ -13,7 +14,6 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
     const [selectedQueryId, setSelectedQueryId] = useState(geneIds.recognizedIds[0] ?? 'auto');
     const [sequenceSearchType, setSequenceSearchType] = useState('md5');
     const [selectedUniprotId, setSelectedUniprotId] = useState();
-    const [userTranscriptId, setUserTranscriptId] = useState();
     const transcriptOptions = getTranscriptFeatures(feature);
     const featureUniprotId = geneIds.uniprotId;
     const effectiveLookupMode = lookupMode === 'auto' && featureUniprotId ? 'feature' : lookupMode;
@@ -38,18 +38,15 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
             : effectiveLookupMode === 'manual'
                 ? debouncedManualUniprotId
                 : undefined;
-    const { predictions, isLoading: isAlphaFoldLoading, error: alphaFoldError, selectedEntryIndex, setSelectedEntryIndex, url: alphaFoldUrl, confidenceUrl: alphaFoldConfidenceUrl, structureSequence: alphaFoldStructureSequence, } = useAlphaFoldData({
+    const { isLoading: isAlphaFoldLoading, error: alphaFoldError, url: alphaFoldUrl, confidenceUrl: alphaFoldConfidenceUrl, structureSequence: alphaFoldStructureSequence, } = useAlphaFoldData({
         uniprotId: isSequenceMode ? undefined : uniprotId,
     });
-    let autoTranscriptId;
-    if (isoformSequences) {
-        autoTranscriptId = selectBestTranscript({
-            options: transcriptOptions,
-            isoformSequences,
-            structureSequence: alphaFoldStructureSequence,
-        })?.id();
-    }
-    const effectiveTranscriptId = userTranscriptId ?? autoTranscriptId;
+    const { userSelection: effectiveTranscriptId, setUserSelection } = useTranscriptSelection({
+        options: transcriptOptions,
+        isoformSequences,
+        structureSequence: alphaFoldStructureSequence,
+        resetKey: uniprotId,
+    });
     const selectedTranscript = transcriptOptions.find(f => getId(f) === effectiveTranscriptId);
     const userSelectedProteinSequence = effectiveTranscriptId
         ? isoformSequences?.[effectiveTranscriptId]
@@ -68,10 +65,6 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         ? seqSearchStructureSequence
         : alphaFoldStructureSequence;
     const finalUniprotId = isSequenceMode ? seqSearchUniprotId : uniprotId;
-    const setSelectedUniprotIdWithReset = (id) => {
-        setSelectedUniprotId(id);
-        setUserTranscriptId(undefined);
-    };
     const loadingStatuses = [
         isLookupLoading && 'Looking up UniProt ID',
         isIsoformLoading && 'Loading protein sequences from transcript isoforms',
@@ -96,17 +89,14 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         sequenceSearchType,
         setSequenceSearchType,
         selectedUniprotId,
-        setSelectedUniprotId: setSelectedUniprotIdWithReset,
+        setSelectedUniprotId,
         userSelection: effectiveTranscriptId,
-        setUserSelection: setUserTranscriptId,
+        setUserSelection,
         transcriptOptions,
         selectedTranscript,
         isoformSequences,
         userSelectedProteinSequence,
         uniprotEntries,
-        predictions,
-        selectedEntryIndex,
-        setSelectedEntryIndex,
         recognizedIds: geneIds.recognizedIds,
         geneName: geneIds.geneName,
         featureUniprotId,
@@ -144,7 +134,6 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
             isAutoMode &&
             !isLookupLoading &&
             uniprotEntries.length === 0,
-        showAlphaFoldEntrySelector: !!predictions && !isSequenceMode,
         showSequenceSearchStatus: isSequenceMode,
         showAlphaFoldDBSearchStatus: !!finalStructureSequence && !!finalUniprotId && !isSequenceMode,
         isLoading,

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

@@ -1,13 +1,8 @@
-export default function useAlphaFoldData({ uniprotId, useApiSearch, }: {
+export default function useAlphaFoldData({ uniprotId }: {
     uniprotId?: string;
-    useApiSearch?: boolean;
 }): {
-    predictions: import("./useAlphaFoldUrl").AlphaFoldPrediction[] | undefined;
     isLoading: boolean;
     error: any;
-    selectedEntryIndex: number;
-    setSelectedEntryIndex: import("react").Dispatch<import("react").SetStateAction<number>>;
-    selectedPrediction: import("./useAlphaFoldUrl").AlphaFoldPrediction | undefined;
     url: string | undefined;
     confidenceUrl: string | undefined;
     structureSequence: string | undefined;

package/dist/LaunchProteinView/hooks/useAlphaFoldData.js

@@ -1,34 +1,18 @@
-import { useState } from 'react';
-import useAlphaFoldUrl from './useAlphaFoldUrl';
 import useRemoteStructureFileSequence from './useRemoteStructureFileSequence';
 import { getAlphaFoldConfidenceUrl, getAlphaFoldStructureUrl, } from '../utils/launchViewUtils';
-export default function useAlphaFoldData({ uniprotId, useApiSearch = false, }) {
-    const [selectedEntryIndex, setSelectedEntryIndex] = useState(0);
-    const hardcodedUrl = uniprotId
-        ? getAlphaFoldStructureUrl(uniprotId)
-        : undefined;
-    const hardcodedConfidenceUrl = uniprotId
+export default function useAlphaFoldData({ uniprotId }) {
+    const url = uniprotId ? getAlphaFoldStructureUrl(uniprotId) : undefined;
+    const confidenceUrl = uniprotId
         ? getAlphaFoldConfidenceUrl(uniprotId)
         : undefined;
-    // Optionally fetch from API for isoform search
-    const { predictions, isLoading: isApiLoading, error: apiError, } = useAlphaFoldUrl({ uniprotId: useApiSearch ? uniprotId : undefined });
-    const selectedPrediction = predictions?.[selectedEntryIndex];
-    const url = useApiSearch ? selectedPrediction?.cifUrl : hardcodedUrl;
-    const confidenceUrl = selectedPrediction?.plddtDocUrl ?? hardcodedConfidenceUrl;
-    // Always fetch sequence from structure file
-    const { sequences, isLoading: isSequenceLoading, error: sequenceError, } = useRemoteStructureFileSequence({ url });
-    const structureSequence = sequences?.[0];
-    const isLoading = isApiLoading || isSequenceLoading;
-    const error = apiError ?? sequenceError;
+    const { sequences, isLoading, error } = useRemoteStructureFileSequence({
+        url,
+    });
     return {
-        predictions,
         isLoading,
         error,
-        selectedEntryIndex,
-        setSelectedEntryIndex,
-        selectedPrediction,
         url,
         confidenceUrl,
-        structureSequence,
+        structureSequence: sequences?.[0],
     };
 }

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

@@ -1,11 +1,12 @@
 import type { Feature } from '@jbrowse/core/util';
-export default function useTranscriptSelection({ options, isoformSequences, structureSequence, }: {
+export default function useTranscriptSelection({ options, isoformSequences, structureSequence, resetKey, }: {
     options: Feature[];
     isoformSequences?: Record<string, {
         feature: Feature;
         seq: string;
     }>;
     structureSequence?: string;
+    resetKey?: string;
 }): {
     userSelection: string | undefined;
     setUserSelection: import("react").Dispatch<import("react").SetStateAction<string | undefined>>;

package/dist/LaunchProteinView/hooks/useTranscriptSelection.js

@@ -1,10 +1,18 @@
 import { useMemo, useState } from 'react';
 import { selectBestTranscript } from '../utils/util';
-export default function useTranscriptSelection({ options, isoformSequences, structureSequence, }) {
+export default function useTranscriptSelection({ options, isoformSequences, structureSequence, resetKey, }) {
     const [userSelection, setUserSelection] = useState();
+    const [prevResetKey, setPrevResetKey] = useState(resetKey);
+    if (resetKey !== prevResetKey) {
+        setPrevResetKey(resetKey);
+        setUserSelection(undefined);
+    }
     const autoSelection = useMemo(() => isoformSequences !== undefined
-        ? selectBestTranscript({ options, isoformSequences, structureSequence })?.id()
+        ? selectBestTranscript({
+            options,
+            isoformSequences,
+            structureSequence,
+        })?.id()
         : undefined, [options, structureSequence, isoformSequences]);
-    const effectiveSelection = userSelection ?? autoSelection;
-    return { userSelection: effectiveSelection, setUserSelection };
+    return { userSelection: userSelection ?? autoSelection, setUserSelection };
 }

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

@@ -1,7 +1,6 @@
 import type { UniProtEntry } from '../services/lookupMethods';
-export default function useUniProtSearch({ recognizedIds, uniprotId, geneId, geneName, selectedQueryId, enabled, }: {
+export default function useUniProtSearch({ recognizedIds, geneId, geneName, selectedQueryId, enabled, }: {
     recognizedIds?: string[];
-    uniprotId?: string;
     geneId?: string;
     geneName?: string;
     selectedQueryId?: string;

package/dist/LaunchProteinView/hooks/useUniProtSearch.js

@@ -1,12 +1,7 @@
 import useSWR from 'swr';
 import { searchUniProtEntries } from '../services/lookupMethods';
 import { isRecognizedDatabaseId } from '../utils/util';
-export default function useUniProtSearch({ recognizedIds = [], uniprotId, geneId, geneName, selectedQueryId = 'auto', enabled = true, }) {
-    // If selected ID is a UniProt accession (prefixed with uniprot:), return it directly
-    const isDirectUniProt = selectedQueryId.startsWith('uniprot:');
-    const directUniProtId = isDirectUniProt
-        ? selectedQueryId.replace('uniprot:', '')
-        : undefined;
+export default function useUniProtSearch({ recognizedIds = [], geneId, geneName, selectedQueryId = 'auto', enabled = true, }) {
     // Determine what to search based on selectedQueryId
     let idsToSearch = [];
     let geneNameToSearch;
@@ -20,16 +15,10 @@ export default function useUniProtSearch({ recognizedIds = [], uniprotId, geneId
     else if (isRecognizedDatabaseId(selectedQueryId)) {
         idsToSearch = [selectedQueryId];
     }
-    // Has valid ID if we have any recognized database IDs or a gene name
-    const hasRecognizedId = idsToSearch.some(id => isRecognizedDatabaseId(id));
-    const hasValidId = hasRecognizedId || Boolean(geneNameToSearch) || Boolean(uniprotId);
-    const { data, error, isLoading } = useSWR(enabled && hasValidId && !isDirectUniProt
-        ? [
-            'uniprotSearch',
-            selectedQueryId,
-            idsToSearch.join(','),
-            geneNameToSearch,
-        ]
+    const hasValidId = idsToSearch.some(id => isRecognizedDatabaseId(id)) ||
+        Boolean(geneNameToSearch);
+    const { data, error, isLoading } = useSWR(enabled && hasValidId
+        ? ['uniprotSearch', selectedQueryId, idsToSearch.join(','), geneNameToSearch]
         : null, async () => searchUniProtEntries({
         recognizedIds: idsToSearch,
         geneId,
@@ -40,15 +29,6 @@ export default function useUniProtSearch({ recognizedIds = [], uniprotId, geneId
         revalidateIfStale: false,
         keepPreviousData: true,
     });
-    // If direct UniProt accession selected, return it as a synthetic entry
-    if (isDirectUniProt && directUniProtId) {
-        return {
-            entries: [{ accession: directUniProtId, isReviewed: true }],
-            isLoading: false,
-            error: undefined,
-            hasValidId: true,
-        };
-    }
     return {
         entries: data ?? [],
         isLoading,

package/dist/LaunchProteinView/utils/launchViewUtils.js

@@ -75,16 +75,7 @@ export function launch3DProteinView({ session, view, feature, selectedTranscript
         displayName: displayName ??
             formatViewName('Protein view', feature, selectedTranscript, uniprotId),
     };
-    // eslint-disable-next-line no-console
-    console.log('[protein3d debug] addView ProteinView snapshot:', JSON.stringify(snap, (_k, v) => (typeof v === 'function' ? '<fn>' : v), 2));
-    try {
-        return session.addView('ProteinView', snap);
-    }
-    catch (e) {
-        // eslint-disable-next-line no-console
-        console.log('[protein3d debug] addView threw:', e.message);
-        throw e;
-    }
+    return session.addView('ProteinView', snap);
 }
 export async function launch1DProteinView({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }) {
     if (!uniprotId || !isSessionWithAddTracks(session)) {