npm - jbrowse-plugin-protein3d - Versions diffs - 0.3.1 → 0.3.3 - Mend

jbrowse-plugin-protein3d 0.3.1 → 0.3.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (146) hide show

package/dist/LaunchProteinView/components/TranscriptSelector.js CHANGED Viewed

@@ -23,7 +23,7 @@ export default function TranscriptSelector({ val, setVal, isoforms, isoformSeque
         isoformSequences[a.id()].seq.length);
     nonMatches.sort((a, b) => isoformSequences[b.id()].seq.length -
         isoformSequences[a.id()].seq.length);
-    return (React.createElement(TextField, { value: val, onChange: event => {
+    return (React.createElement(TextField, { value: val ?? '', onChange: event => {
             setVal(event.target.value);
         }, label: "Choose transcript isoform", select: true, disabled: disabled },
         matches.map(f => (React.createElement(MenuItem, { value: f.id(), key: f.id() },

package/dist/LaunchProteinView/components/TranscriptSelector.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAEnD,OAAO,EACL,kBAAkB,EAClB,wBAAwB,EACxB,cAAc,GACf,MAAM,eAAe,CAAA;AAItB,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,GAAG,EACH,MAAM,EACN,QAAQ,EACR,gBAAgB,EAChB,iBAAiB,EACjB,OAAO,EACP,QAAQ,GAST;IACC,MAAM,QAAQ,GAAG,kBAAkB,CAAC,OAAO,CAAC,CAAA;IAC5C,MAAM,OAAO,GAAc,EAAE,CAAA;IAC7B,MAAM,UAAU,GAAc,EAAE,CAAA;IAChC,MAAM,MAAM,GAAc,EAAE,CAAA;IAE5B,KAAK,MAAM,CAAC,IAAI,QAAQ,EAAE,CAAC;QACzB,MAAM,KAAK,GAAG,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;QACtC,IAAI,CAAC,KAAK,EAAE,CAAC;YACX,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChB,CAAC;aAAM,IACL,iBAAiB;YACjB,cAAc,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,iBAAiB,EAC/C,CAAC;YACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IAED,OAAO,CAAC,IAAI,CACV,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;QACpC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM,CACvC,CAAA;IACD,UAAU,CAAC,IAAI,CACb,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;QACpC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM,CACvC,CAAA;IAED,OAAO,CACL,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,IAAI,EAAE,EAChB,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,EACD,KAAK,EAAC,2BAA2B,EACjC,MAAM,QACN,QAAQ,EAAE,QAAQ;QAEjB,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAChB,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE;YACjC,QAAQ;;YAAK,wBAAwB,CAAC,CAAC,CAAC;;YACxC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;+CAC5B,CACZ,CAAC;QACD,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACnB,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE;YACjC,QAAQ;;YAAK,wBAAwB,CAAC,CAAC,CAAC;;YACxC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;kBAC5B,CACZ,CAAC;QACD,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACf,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,QAAQ;YAC3C,QAAQ;;YAAK,wBAAwB,CAAC,CAAC,CAAC;yBAChC,CACZ,CAAC,CACQ,CACb,CAAA;AACH,CAAC"}

package/dist/LaunchProteinView/components/UserProvidedStructure.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import React, { useMemo, useState } from 'react';
+import React, { useState } from 'react';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 import { getContainingView, getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
@@ -41,9 +41,7 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
     const [submitError, setSubmitError] = useState();
     const [structureURL, setStructureURL] = useState('');
     const [showAllProteinSequences, setShowAllProteinSequences] = useState(false);
-    // 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 = useMemo(() => getTranscriptFeatures(feature), [feature]);
+    const options = getTranscriptFeatures(feature);
     const view = getContainingView(model);
     const { isoformSequences, error: isoformError } = useIsoformProteinSequences({
         feature,
@@ -60,7 +58,7 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
         structureSequence,
     });
     const selectedTranscript = options.find(val => getId(val) === userSelection);
-    const protein = isoformSequences?.[userSelection ?? ''];
+    const protein = userSelection ? isoformSequences?.[userSelection] : undefined;
     const error = isoformError ?? submitError ?? localFileError ?? remoteFileError;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
@@ -98,7 +96,7 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
                         setStructureURL(`https://files.rcsb.org/download/${s}.cif`);
                     }, label: "PDB ID" })) : null),
             React.createElement("div", { style: { margin: 20 } }, isoformSequences ? (structureSequence ? (React.createElement(React.Fragment, null,
-                React.createElement(TranscriptSelector, { val: userSelection ?? '', setVal: setUserSelection, structureSequence: structureSequence, isoforms: options, feature: feature, isoformSequences: isoformSequences }),
+                React.createElement(TranscriptSelector, { val: userSelection, setVal: setUserSelection, structureSequence: structureSequence, isoforms: options, feature: feature, isoformSequences: isoformSequences }),
                 React.createElement("div", { style: { margin: 10 } },
                     React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
                             setShowAllProteinSequences(!showAllProteinSequences);

package/dist/LaunchProteinView/components/UserProvidedStructure.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"UserProvidedStructure.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/UserProvidedStructure.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAClE,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,KAAK,EACL,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,0BAA0B,EAAE,MAAM,yBAAyB,CAAA;AACpE,OAAO,YAAY,MAAM,+BAA+B,CAAA;AACxD,OAAO,0BAA0B,MAAM,qCAAqC,CAAA;AAC5E,OAAO,6BAA6B,MAAM,wCAAwC,CAAA;AAClF,OAAO,8BAA8B,MAAM,yCAAyC,CAAA;AACpF,OAAO,sBAAsB,MAAM,iCAAiC,CAAA;AACpE,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAA;AAC9D,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,EACrB,cAAc,GACf,MAAM,eAAe,CAAA;AAMtB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,aAAa,EAAE;QACb,SAAS,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC3B,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAC,CAAA;AAIH,SAAS,QAAQ;IACf,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE;;QAE6C,GAAG;QAC9E,oBAAC,YAAY,IAAC,IAAI,EAAC,wCAAwC,gBAE5C;4MAIX,CACP,CAAA;AACH,CAAC;AAED,MAAM,qBAAqB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACpE,OAAO,EACP,KAAK,EACL,WAAW,EACX,kBAAkB,EAClB,0BAA0B,GAO3B;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,EAAQ,CAAA;IACxC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACtC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5C,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,EAAW,CAAA;IACzD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACpD,MAAM,CAAC,uBAAuB,EAAE,0BAA0B,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAE7E,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAAQ,CAAA;IAC5C,MAAM,EAAE,gBAAgB,EAAE,KAAK,EAAE,YAAY,EAAE,GAAG,0BAA0B,CAAC;QAC3E,OAAO;QACP,IAAI;KACL,CAAC,CAAA;IACF,MAAM,EAAE,SAAS,EAAE,mBAAmB,EAAE,KAAK,EAAE,cAAc,EAAE,GAC7D,6BAA6B,CAAC,EAAE,IAAI,EAAE,CAAC,CAAA;IACzC,MAAM,EAAE,SAAS,EAAE,mBAAmB,EAAE,KAAK,EAAE,eAAe,EAAE,GAC9D,8BAA8B,CAAC,EAAE,GAAG,EAAE,YAAY,EAAE,CAAC,CAAA;IAEvD,MAAM,aAAa,GACjB,IAAI,EAAE,IAAI,IAAI,YAAY,CAAC,KAAK,CAAC,YAAY,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;IACrE,MAAM,kBAAkB,GAAG,mBAAmB,IAAI,mBAAmB,CAAA;IACrE,MAAM,iBAAiB,GAAG,kBAAkB,EAAE,CAAC,CAAC,CAAC,CAAA;IAEjD,MAAM,EAAE,aAAa,EAAE,gBAAgB,EAAE,GAAG,sBAAsB,CAAC;QACjE,OAAO;QACP,gBAAgB;QAChB,iBAAiB;KAClB,CAAC,CAAA;IACF,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,aAAa,CAAC,CAAA;IAC5E,MAAM,OAAO,GAAG,aAAa,CAAC,CAAC,CAAC,gBAAgB,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAE7E,MAAM,KAAK,GAAG,YAAY,IAAI,WAAW,IAAI,cAAc,IAAI,eAAe,CAAA;IAC9E,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,QAAQ,OAAG;YAEZ,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE;gBACzC,oBAAC,UAAU;;oBACgB,oBAAC,UAAU,OAAG,CAC5B;gBAEb,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;oBAC/B,oBAAC,UAAU,IACT,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,KAAK,CAAC,EAAE;4BAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;wBAC/B,CAAC;wBAED,oBAAC,gBAAgB,IAAC,KAAK,EAAC,KAAK,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,KAAK,GAAG;wBAChE,oBAAC,gBAAgB,IAAC,KAAK,EAAC,MAAM,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,MAAM,GAAG;wBAClE,oBAAC,gBAAgB,IACf,KAAK,EAAC,KAAK,EACX,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,QAAQ,GACd,CACS,CACD;gBACb,MAAM,KAAK,KAAK,CAAC,CAAC,CAAC,CAClB;oBACE,oBAAC,UAAU,qDAEE;oBACb,oBAAC,SAAS,IACR,KAAK,EAAC,KAAK,EACX,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;4BAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;wBACrC,CAAC,GACD,CACE,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,MAAM,KAAK,MAAM,CAAC,CAAC,CAAC,CACnB,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE;oBAC5B,oBAAC,UAAU,2DAEE;oBACb,oBAAC,MAAM,IAAC,OAAO,EAAC,UAAU,EAAC,SAAS,EAAC,OAAO;;wBAE1C,+BACE,IAAI,EAAC,MAAM,EACX,MAAM,QACN,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE;gCACvB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;gCAC9B,IAAI,IAAI,EAAE,CAAC;oCACT,OAAO,CAAC,IAAI,CAAC,CAAA;gCACf,CAAC;4BACH,CAAC,GACD,CACK,CACL,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,MAAM,KAAK,KAAK,CAAC,CAAC,CAAC,CAClB,oBAAC,SAAS,IACR,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,KAAK,CAAA;wBAC5B,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACX,eAAe,CAAC,mCAAmC,CAAC,MAAM,CAAC,CAAA;oBAC7D,CAAC,EACD,KAAK,EAAC,QAAQ,GACd,CACH,CAAC,CAAC,CAAC,IAAI,CACJ;YACN,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,IACvB,gBAAgB,CAAC,CAAC,CAAC,CAClB,iBAAiB,CAAC,CAAC,CAAC,CAClB;gBACE,oBAAC,kBAAkB,IACjB,GAAG,EAAE,aAAa,EAClB,MAAM,EAAE,gBAAgB,EACxB,iBAAiB,EAAE,iBAAiB,EACpC,QAAQ,EAAE,OAAO,EACjB,OAAO,EAAE,OAAO,EAChB,gBAAgB,EAAE,gBAAgB,GAClC;gBACF,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;oBACxB,oBA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package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.d.ts CHANGED Viewed

@@ -15,7 +15,7 @@ export default function useAlphaFoldDBSearch({ feature, view, }: {
     sequenceSearchType: SequenceSearchType;
     setSequenceSearchType: import("react").Dispatch<import("react").SetStateAction<SequenceSearchType>>;
     selectedUniprotId: string | undefined;
-    setSelectedUniprotId: import("react").Dispatch<import("react").SetStateAction<string | undefined>>;
+    setSelectedUniprotId: (id: string | undefined) => void;
     userSelection: string | undefined;
     setUserSelection: import("react").Dispatch<import("react").SetStateAction<string | undefined>>;
     transcriptOptions: Feature[];

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import { useEffect, useMemo, useState } from 'react';
+import { useState } from 'react';
 import useAlphaFoldData from './useAlphaFoldData';
 import useAlphaFoldSequenceSearch from './useAlphaFoldSequenceSearch';
 import useIsoformProteinSequences from './useIsoformProteinSequences';
@@ -8,17 +8,13 @@ import { extractFeatureIdentifiers, getId, getTranscriptFeatures, getUniProtIdFr
 export default function useAlphaFoldDBSearch({ feature, view, }) {
     const [lookupMode, setLookupMode] = useState('auto');
     const [manualUniprotId, setManualUniprotId] = useState('');
-    const [selectedQueryId, setSelectedQueryId] = useState('auto');
+    const geneIds = extractFeatureIdentifiers(feature);
+    const [selectedQueryId, setSelectedQueryId] = useState(geneIds.recognizedIds[0] ?? 'auto');
     const [sequenceSearchType, setSequenceSearchType] = useState('md5');
     const [selectedUniprotId, setSelectedUniprotId] = useState();
     const [userTranscriptId, setUserTranscriptId] = useState();
-    // Gene-level identifiers for the UniProt search
-    const transcriptOptions = useMemo(() => getTranscriptFeatures(feature), [feature]);
-    const geneIds = useMemo(() => extractFeatureIdentifiers(feature), [feature]);
+    const transcriptOptions = getTranscriptFeatures(feature);
     const featureUniprotId = getUniProtIdFromFeature(feature);
-    // Compute effective lookup mode synchronously — avoids a useEffect that
-    // would leave a one-frame gap where isLoading is false but uniprotId is
-    // still undefined
     const effectiveLookupMode = lookupMode === 'auto' && featureUniprotId ? 'feature' : lookupMode;
     const isSequenceMode = effectiveLookupMode === 'sequence';
     const isAutoMode = effectiveLookupMode === 'auto';
@@ -41,23 +37,19 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
     const { predictions, isLoading: isAlphaFoldLoading, error: alphaFoldError, selectedEntryIndex, setSelectedEntryIndex, url: alphaFoldUrl, confidenceUrl: alphaFoldConfidenceUrl, structureSequence: alphaFoldStructureSequence, } = useAlphaFoldData({
         uniprotId: isSequenceMode ? undefined : uniprotId,
     });
-    // SYNC: src/LaunchProteinView/hooks/useTranscriptSelection.ts (same pattern)
-    // Auto-select transcript synchronously — avoids a useEffect that would
-    // leave a one-frame gap where isLoading is false but no transcript is
-    // selected yet
-    const autoTranscriptId = useMemo(() => {
-        if (isoformSequences) {
-            return selectBestTranscript({
-                options: transcriptOptions,
-                isoformSequences,
-                structureSequence: alphaFoldStructureSequence,
-            })?.id();
-        }
-        return undefined;
-    }, [transcriptOptions, alphaFoldStructureSequence, isoformSequences]);
+    let autoTranscriptId;
+    if (isoformSequences) {
+        autoTranscriptId = selectBestTranscript({
+            options: transcriptOptions,
+            isoformSequences,
+            structureSequence: alphaFoldStructureSequence,
+        })?.id();
+    }
     const effectiveTranscriptId = userTranscriptId ?? autoTranscriptId;
     const selectedTranscript = transcriptOptions.find(f => getId(f) === effectiveTranscriptId);
-    const userSelectedProteinSequence = isoformSequences?.[effectiveTranscriptId ?? ''];
+    const userSelectedProteinSequence = effectiveTranscriptId
+        ? isoformSequences?.[effectiveTranscriptId]
+        : undefined;
     const { uniprotId: seqSearchUniprotId, cifUrl: seqSearchUrl, plddtDocUrl: seqSearchConfidenceUrl, structureSequence: seqSearchStructureSequence, isLoading: isSequenceSearchLoading, error: sequenceSearchError, } = useAlphaFoldSequenceSearch({
         sequence: userSelectedProteinSequence?.seq,
         searchType: sequenceSearchType,
@@ -72,10 +64,10 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         ? seqSearchStructureSequence
         : alphaFoldStructureSequence;
     const finalUniprotId = isSequenceMode ? seqSearchUniprotId : uniprotId;
-    // Reset manual transcript selection when UniProt selection changes
-    useEffect(() => {
+    const setSelectedUniprotIdWithReset = (id) => {
+        setSelectedUniprotId(id);
         setUserTranscriptId(undefined);
-    }, [selectedUniprotId]);
+    };
     const loadingStatuses = [
         isLookupLoading && 'Looking up UniProt ID',
         isIsoformLoading && 'Loading protein sequences from transcript isoforms',
@@ -100,7 +92,7 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         sequenceSearchType,
         setSequenceSearchType,
         selectedUniprotId,
-        setSelectedUniprotId,
+        setSelectedUniprotId: setSelectedUniprotIdWithReset,
         userSelection: effectiveTranscriptId,
         setUserSelection: setUserTranscriptId,
         transcriptOptions,

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/LaunchProteinView/hooks/useAlphaFoldData.d.ts CHANGED Viewed

@@ -1,6 +1,3 @@
-/**
- * Custom hook to manage AlphaFold predictions and selected entry
- */
 export default function useAlphaFoldData({ uniprotId, useApiSearch, }: {
     uniprotId?: string;
     useApiSearch?: boolean;

package/dist/LaunchProteinView/hooks/useAlphaFoldData.js CHANGED Viewed

@@ -1,20 +1,20 @@
-import { useMemo, useState } from 'react';
+import { useState } from 'react';
 import useAlphaFoldUrl from './useAlphaFoldUrl';
 import useRemoteStructureFileSequence from './useRemoteStructureFileSequence';
-import { getAlphaFoldStructureUrl } from '../utils/launchViewUtils';
-/**
- * Custom hook to manage AlphaFold predictions and selected entry
- */
+import { getAlphaFoldConfidenceUrl, getAlphaFoldStructureUrl, } from '../utils/launchViewUtils';
 export default function useAlphaFoldData({ uniprotId, useApiSearch = false, }) {
     const [selectedEntryIndex, setSelectedEntryIndex] = useState(0);
-    const hardcodedUrl = useMemo(() => (uniprotId ? getAlphaFoldStructureUrl(uniprotId) : undefined), [uniprotId]);
+    const hardcodedUrl = uniprotId
+        ? getAlphaFoldStructureUrl(uniprotId)
+        : undefined;
+    const hardcodedConfidenceUrl = 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];
-    // When using API, use the selected prediction's URL
-    // Otherwise, use the hardcoded URL
     const url = useApiSearch ? selectedPrediction?.cifUrl : hardcodedUrl;
-    const confidenceUrl = selectedPrediction?.plddtDocUrl;
+    const confidenceUrl = selectedPrediction?.plddtDocUrl ?? hardcodedConfidenceUrl;
     // Always fetch sequence from structure file
     const { sequences, isLoading: isSequenceLoading, error: sequenceError, } = useRemoteStructureFileSequence({ url });
     const structureSequence = sequences?.[0];

package/dist/LaunchProteinView/hooks/useAlphaFoldData.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchProteinView/hooks/useFoldseekSearch.d.ts CHANGED Viewed

@@ -11,6 +11,6 @@ export default function useFoldseekSearch(): {
         aaSequence: string;
         di3Sequence: string;
     } | undefined>;
-    search: (aaSeq: string, di3Seq: string, databases?: FoldseekDatabaseId[]) => Promise<void>;
+    search: (aaSeq: string, di3Seq: string, databases?: FoldseekDatabaseId[]) => Promise<FoldseekResult | undefined>;
     reset: () => void;
 };

package/dist/LaunchProteinView/hooks/useFoldseekSearch.js CHANGED Viewed

@@ -1,88 +1,59 @@
-import { useCallback, useEffect, useRef, useState } from 'react';
+import { useState } from 'react';
 import { DEFAULT_DATABASES, predict3Di, submitFoldseekSearch, waitForFoldseekResults, } from '../services/foldseekApi';
 export default function useFoldseekSearch() {
     const [results, setResults] = useState();
-    const [cleanedAaSequence, setCleanedAaSequence] = useState();
-    const [di3Sequence, setDi3Sequence] = useState();
+    const [predictData, setPredictData] = useState();
     const [isLoading, setIsLoading] = useState(false);
     const [isPredicting, setIsPredicting] = useState(false);
     const [error, setError] = useState();
     const [statusMessage, setStatusMessage] = useState('');
-    const abortRef = useRef(false);
-    useEffect(() => {
-        return () => {
-            abortRef.current = true;
-        };
-    }, []);
-    const predictStructure = useCallback(async (aaSequence) => {
+    const predictStructure = async (aaSequence) => {
         setIsPredicting(true);
         setError(undefined);
-        setCleanedAaSequence(undefined);
-        setDi3Sequence(undefined);
         setStatusMessage('Predicting 3Di structure...');
         try {
             const result = await predict3Di(aaSequence);
-            setCleanedAaSequence(result.aaSequence);
-            setDi3Sequence(result.di3Sequence);
-            setStatusMessage('');
+            setPredictData(result);
             return result;
         }
         catch (e) {
             setError(e);
-            setStatusMessage('');
             return undefined;
         }
         finally {
             setIsPredicting(false);
+            setStatusMessage('');
         }
-    }, []);
-    const search = useCallback(async (aaSeq, di3Seq, databases = DEFAULT_DATABASES) => {
-        const isAborted = () => abortRef.current;
+    };
+    const search = async (aaSeq, di3Seq, databases = DEFAULT_DATABASES) => {
         setIsLoading(true);
         setError(undefined);
-        setResults(undefined);
         setStatusMessage('Submitting search...');
-        abortRef.current = false;
         try {
             const ticket = await submitFoldseekSearch(aaSeq, di3Seq, databases);
-            if (isAborted()) {
-                return;
-            }
-            const results = await waitForFoldseekResults(ticket.id, databases, status => {
-                if (!isAborted()) {
-                    setStatusMessage(status);
-                }
-            });
-            if (!isAborted()) {
-                setResults(results);
-                setStatusMessage('');
-            }
+            const result = await waitForFoldseekResults(ticket.id, databases, setStatusMessage);
+            setResults(result);
+            return result;
         }
         catch (e) {
-            if (!isAborted()) {
-                setError(e);
-                setStatusMessage('');
-            }
+            setError(e);
+            return undefined;
         }
         finally {
-            if (!isAborted()) {
-                setIsLoading(false);
-            }
+            setIsLoading(false);
+            setStatusMessage('');
         }
-    }, []);
-    const reset = useCallback(() => {
+    };
+    const reset = () => {
         setResults(undefined);
-        setCleanedAaSequence(undefined);
-        setDi3Sequence(undefined);
+        setPredictData(undefined);
         setError(undefined);
-        setIsLoading(false);
-        setIsPredicting(false);
         setStatusMessage('');
-    }, []);
+    };
     return {
         results,
-        cleanedAaSequence,
-        di3Sequence,
+        cleanedAaSequence: predictData?.aaSequence,
+        di3Sequence: predictData?.di3Sequence,
         isLoading,
         isPredicting,
         error,

package/dist/LaunchProteinView/hooks/useFoldseekSearch.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchProteinView/hooks/useLocalStorage.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import { useEffect, useState } from 'react';
+import { useState } from 'react';
 export function useLocalStorage(key, defaultValue) {
     const [value, setValue] = useState(() => {
         const stored = localStorage.getItem(key);
@@ -12,9 +12,10 @@ export function useLocalStorage(key, defaultValue) {
         }
         return defaultValue;
     });
-    useEffect(() => {
-        localStorage.setItem(key, JSON.stringify(value));
-    }, [key, value]);
-    return [value, setValue];
+    function setValueAndStore(newValue) {
+        setValue(newValue);
+        localStorage.setItem(key, JSON.stringify(newValue));
+    }
+    return [value, setValueAndStore];
 }
 //# sourceMappingURL=useLocalStorage.js.map

package/dist/LaunchProteinView/hooks/useLocalStorage.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchProteinView/hooks/useLocalStructureFileSequence.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchProteinView/index.js CHANGED Viewed

@@ -10,13 +10,7 @@ function extendStateModel(stateModel) {
         return {
             contextMenuItems() {
                 const feature = self.contextMenuFeature;
-                const track = getContainingTrack(self);
-                // DO NOT DELETE: contextMenuInfo must be captured here, not inside
-                // onClick. The canvas display clears contextMenuInfo when the context
-                // menu closes, which happens before onClick fires. Capturing it here
-                // in the view ensures the regionNumber is available in the closure.
-                const contextMenuInfo = self.contextMenuInfo;
-                const showProteinMenuItem = feature &&
+                const showProteinMenuItem = feature !== undefined &&
                     ['gene', 'mRNA', 'transcript'].includes(feature.get('type'));
                 return [
                     ...superContextMenuItems(),
@@ -26,32 +20,12 @@ function extendStateModel(stateModel) {
                                 label: 'Launch protein view',
                                 icon: AddIcon,
                                 onClick: () => {
+                                    const track = getContainingTrack(self);
                                     const session = getSession(track);
-                                    const openDialog = (f) => {
-                                        session.queueDialog(handleClose => [
-                                            LaunchProteinViewDialog,
-                                            { model: track, handleClose, feature: f },
-                                        ]);
-                                    };
-                                    if (self.fetchFullFeature && contextMenuInfo) {
-                                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                                        ;
-                                        (async () => {
-                                            try {
-                                                const fullFeature = await self.fetchFullFeature(feature.id(), contextMenuInfo.regionNumber);
-                                                if (fullFeature) {
-                                                    openDialog(fullFeature);
-                                                }
-                                            }
-                                            catch (e) {
-                                                console.error(e);
-                                                session.notify(`${e}`, 'error');
-                                            }
-                                        })();
-                                    }
-                                    else {
-                                        openDialog(feature);
-                                    }
+                                    session.queueDialog(handleClose => [
+                                        LaunchProteinViewDialog,
+                                        { model: track, handleClose, feature },
+                                    ]);
                                 },
                             },
                         ]

package/dist/LaunchProteinView/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchProteinView/services/lookupMethods.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-import { isRecognizedDatabaseId } from '../utils/util';
 export interface UniProtEntry {
     accession: string;
     id?: string;
@@ -7,7 +6,6 @@ export interface UniProtEntry {
     proteinName?: string;
     isReviewed: boolean;
 }
-export { isRecognizedDatabaseId as isRecognizedTranscriptId };
 /**
  * Search UniProt for entries matching a gene, returning multiple results.
  * Tries multiple strategies in order of specificity:
@@ -20,3 +18,4 @@ export declare function searchUniProtEntries({ recognizedIds, geneId, geneName,
     geneName?: string;
     organismId?: number;
 }): Promise<UniProtEntry[]>;
+export { isRecognizedDatabaseId as isRecognizedTranscriptId } from '../utils/util';

package/dist/LaunchProteinView/services/lookupMethods.js CHANGED Viewed

@@ -1,7 +1,6 @@
 import { jsonfetch } from '../../fetchUtils';
 import { getDatabaseTypeForId, isRecognizedDatabaseId, stripTrailingVersion, } from '../utils/util';
 // Re-export for backward compatibility
-export { isRecognizedDatabaseId as isRecognizedTranscriptId };
 const UNIPROT_FIELDS = 'accession,id,gene_names,organism_name,protein_name,reviewed';
 function mapApiResultToEntry(result) {
     return {
@@ -89,4 +88,5 @@ export async function searchUniProtEntries({ recognizedIds = [], geneId, geneNam
     // Sort reviewed entries first
     return entries.toSorted((a, b) => Number(b.isReviewed) - Number(a.isReviewed));
 }
+export { isRecognizedDatabaseId as isRecognizedTranscriptId } from '../utils/util';
 //# sourceMappingURL=lookupMethods.js.map

package/dist/LaunchProteinView/services/lookupMethods.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchProteinView/utils/launchViewUtils.js CHANGED Viewed

@@ -107,7 +107,7 @@ export function launchMsaView({ session, view, feature, selectedTranscript, unip
     });
 }
 export function hasMsaViewPlugin() {
-    return typeof window.JBrowsePluginMsaView !== 'undefined';
+    return window.JBrowsePluginMsaView !== undefined;
 }
 export function launch3DProteinViewWithMsa(params) {
     const { session, view, feature, selectedTranscript, uniprotId } = params;

package/dist/LaunchProteinView/utils/launchViewUtils.js.map CHANGED Viewed

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