Updates

Author: cmdcolin

src/LaunchProteinView/components/UserProvidedStructure.tsx

@@ -233,7 +233,7 @@ const UserProvidedStructure = observer(function UserProvidedStructure({
         </div>
       </DialogContent>
       <DialogActions>
-        {protein?.seq.replaceAll('*', '') !== structureSequence ? (
+        {protein?.seq && structureSequence && protein.seq.replaceAll('*', '') !== structureSequence ? (
           <Typography
             variant="body2"
             sx={{ mr: 2, display: 'flex', alignItems: 'center' }}

src/LaunchProteinView/services/lookupMethods.ts

@@ -87,11 +87,35 @@ async function searchUniProt(
   return data.results.map(mapApiResultToEntry)
 }
 
+async function searchByXref(id: string) {
+  const query = buildXrefQuery(id)
+  if (query) {
+    try {
+      return await searchUniProt(query)
+    } catch (e) {
+      console.error(`xref search failed for ${id}:`, e)
+    }
+  }
+  return []
+}
+
+function deduplicateEntries(entries: UniProtEntry[]) {
+  const seen = new Set<string>()
+  const result: UniProtEntry[] = []
+  for (const entry of entries) {
+    if (!seen.has(entry.accession)) {
+      seen.add(entry.accession)
+      result.push(entry)
+    }
+  }
+  return result
+}
+
 /**
  * Search UniProt for entries matching a gene, returning multiple results.
  * Tries multiple strategies in order of specificity:
  * 1. Recognized database IDs (Ensembl, RefSeq, CCDS, HGNC) via xref search
- * 2. Gene name search
+ * 2. Gene name search (fallback if no reviewed entries found)
  */
 export async function searchUniProtEntries({
   recognizedIds = [],
@@ -103,72 +127,29 @@ export async function searchUniProtEntries({
   geneId?: string
   geneName?: string
   organismId?: number
-}): Promise<UniProtEntry[]> {
-  const entries: UniProtEntry[] = []
-  const seenAccessions = new Set<string>()
-
-  const addEntries = (newEntries: UniProtEntry[]) => {
-    for (const entry of newEntries) {
-      if (!seenAccessions.has(entry.accession)) {
-        seenAccessions.add(entry.accession)
-        entries.push(entry)
-      }
-    }
-  }
-
-  // Strategy 1: Search by recognized database IDs (most specific)
-  for (const id of recognizedIds) {
-    const query = buildXrefQuery(id)
-    if (query) {
-      try {
-        const results = await searchUniProt(query)
-        addEntries(results)
-        if (results.some(e => e.isReviewed)) {
-          break
-        }
-      } catch {
-        // xref search failed, continue to next ID
-      }
-    }
-  }
-
-  // Strategy 2: Try legacy gene_id if it looks like a recognized database ID
+}) {
+  // Collect all IDs to search, including legacy geneId if applicable
+  const idsToSearch = new Set(recognizedIds)
   const strippedGeneId = geneId ? stripTrailingVersion(geneId) : undefined
-  if (
-    strippedGeneId &&
-    isRecognizedDatabaseId(strippedGeneId) &&
-    !recognizedIds.includes(strippedGeneId)
-  ) {
-    const query = buildXrefQuery(strippedGeneId)
-    if (query) {
-      try {
-        addEntries(await searchUniProt(query))
-      } catch {
-        // xref search failed
-      }
-    }
+  if (strippedGeneId && isRecognizedDatabaseId(strippedGeneId)) {
+    idsToSearch.add(strippedGeneId)
   }
 
-  // Strategy 3: If no reviewed entries found, try gene name search
+  // Search all xrefs in parallel
+  const xrefResults = await Promise.all([...idsToSearch].map(searchByXref))
+  let entries = deduplicateEntries(xrefResults.flat())
+
+  // Fallback: if no reviewed entries found, try gene name search
   if (!entries.some(e => e.isReviewed) && geneName) {
     try {
       const query = `gene:${geneName}+AND+organism_id:${organismId}+AND+reviewed:true`
-      addEntries(await searchUniProt(query, 5))
-    } catch {
-      // gene name search failed
+      const geneNameResults = await searchUniProt(query, 5)
+      entries = deduplicateEntries([...entries, ...geneNameResults])
+    } catch (e) {
+      console.error(`gene name search failed for ${geneName}:`, e)
     }
   }
 
   // Sort reviewed entries first
-  entries.sort((a, b) => {
-    if (a.isReviewed && !b.isReviewed) {
-      return -1
-    }
-    if (!a.isReviewed && b.isReviewed) {
-      return 1
-    }
-    return 0
-  })
-
-  return entries
+  return entries.toSorted((a, b) => Number(b.isReviewed) - Number(a.isReviewed))
 }

src/ProteinView/components/ProteinFeatureTrack.tsx

@@ -47,6 +47,21 @@ const FeatureBar = observer(function FeatureBar({
     }
   }
 
+  const highlightAlignmentRange = () => {
+    const { structurePositionToAlignmentMap } = model
+    if (!structurePositionToAlignmentMap) {
+      return
+    }
+    const startAlignmentPos = structurePositionToAlignmentMap[feature.start - 1]
+    const endAlignmentPos = structurePositionToAlignmentMap[feature.end - 1]
+    if (startAlignmentPos !== undefined && endAlignmentPos !== undefined) {
+      model.setAlignmentHoverRange({
+        start: startAlignmentPos,
+        end: endAlignmentPos,
+      })
+    }
+  }
+
   const handleMouseEnter = () => {
     setIsHovered(true)
     const structure = model.molstarStructure
@@ -59,12 +74,14 @@ const FeatureBar = observer(function FeatureBar({
       })
     }
     highlightGenomeRange()
+    highlightAlignmentRange()
   }
 
   const handleMouseLeave = () => {
     setIsHovered(false)
     molstarPluginContext?.managers.interactivity.lociHighlights.clearHighlights()
     model.clearHoverGenomeHighlights()
+    model.clearAlignmentHoverRange()
   }
 
   const handleClick = () => {

src/ProteinView/components/SplitString.tsx

@@ -79,6 +79,40 @@ const HoverHighlight = observer(function HoverHighlight({
   )
 })
 
+const RangeHoverHighlight = observer(function RangeHoverHighlight({
+  model,
+  strLength,
+}: {
+  model: JBrowsePluginProteinStructureModel
+  strLength: number
+}) {
+  const { alignmentHoverRange } = model
+  if (!alignmentHoverRange) {
+    return null
+  }
+  const { start, end } = alignmentHoverRange
+  const clampedStart = Math.max(0, start)
+  const clampedEnd = Math.min(strLength - 1, end)
+  if (clampedStart > clampedEnd) {
+    return null
+  }
+  const width = (clampedEnd - clampedStart + 1) * CHAR_WIDTH
+
+  return (
+    <span
+      style={{
+        position: 'absolute',
+        left: clampedStart * CHAR_WIDTH,
+        top: 0,
+        width,
+        height: '100%',
+        background: 'rgba(255, 165, 0, 0.4)',
+        pointerEvents: 'none',
+      }}
+    />
+  )
+})
+
 const SplitString = observer(function SplitString({
   model,
   str,
@@ -135,6 +169,7 @@ const SplitString = observer(function SplitString({
     >
       <MatchOverlays model={model} />
       <CharacterSpans str={str} />
+      <RangeHoverHighlight model={model} strLength={str.length} />
       <HoverHighlight model={model} strLength={str.length} />
     </span>
   )

src/ProteinView/structureModel.ts

@@ -143,6 +143,13 @@ const Structure = types
      * Tracks whether this structure has been loaded into Molstar
      */
     loadedToMolstar: false,
+    /**
+     * #volatile
+     * Range of alignment positions to highlight (e.g., when hovering a protein feature)
+     */
+    alignmentHoverRange: undefined as
+      | { start: number; end: number }
+      | undefined,
   }))
   .actions(self => ({
     setSequences(str?: string[]) {
@@ -199,6 +206,18 @@ const Structure = types
     clearHoverGenomeHighlights() {
       self.hoverGenomeHighlights = []
     },
+    /**
+     * #action
+     */
+    setAlignmentHoverRange(range?: { start: number; end: number }) {
+      self.alignmentHoverRange = range
+    },
+    /**
+     * #action
+     */
+    clearAlignmentHoverRange() {
+      self.alignmentHoverRange = undefined
+    },
     /**
      * #action
      */

src/ProteinView/util.test.ts

@@ -0,0 +1,41 @@
+import { expect, test } from 'vitest'
+
+import { invertMap } from './util'
+
+test('invertMap - simple case', () => {
+  const map = { 0: 10, 1: 20, 2: 30 }
+  const inverted = invertMap(map)
+  expect(inverted[10]).toBe(0)
+  expect(inverted[20]).toBe(1)
+  expect(inverted[30]).toBe(2)
+})
+
+test('invertMap - empty map', () => {
+  const map = {}
+  const inverted = invertMap(map)
+  expect(Object.keys(inverted)).toHaveLength(0)
+})
+
+test('invertMap - non-sequential values', () => {
+  const map = { 5: 100, 10: 200, 15: 300 }
+  const inverted = invertMap(map)
+  expect(inverted[100]).toBe(5)
+  expect(inverted[200]).toBe(10)
+  expect(inverted[300]).toBe(15)
+})
+
+test('invertMap - alignment position mapping inversion', () => {
+  // Simulates inverting structurePositionToAlignmentMap
+  // structure pos -> alignment pos
+  const structureToAlignment = { 0: 2, 1: 3, 2: 4, 3: 5 }
+  // alignment pos -> structure pos
+  const alignmentToStructure = invertMap(structureToAlignment)
+
+  expect(alignmentToStructure[2]).toBe(0)
+  expect(alignmentToStructure[3]).toBe(1)
+  expect(alignmentToStructure[4]).toBe(2)
+  expect(alignmentToStructure[5]).toBe(3)
+  // positions 0,1 in alignment have no structure mapping
+  expect(alignmentToStructure[0]).toBeUndefined()
+  expect(alignmentToStructure[1]).toBeUndefined()
+})

src/__snapshots__/mappings.test.ts.snap

@@ -899,7 +899,7 @@ exports[`mapping 1`] = `
 }
 `;
 
-exports[`test 1`] = `
+exports[`structureSeqVsTranscriptSeqMap snapshot 1`] = `
 {
   "structureSeqToTranscriptSeqPosition": {
     "0": 392,