jbrowse-plugin-msaview 2.3.2 → 2.3.5

package/src/MsaViewPanel/model.ts

@@ -123,24 +123,31 @@ export default function stateModelFactory() {
       }),
     )
 
-    .volatile(() => ({
-      /**
-       * #volatile
-       */
-      rid: undefined as string | undefined,
-      /**
-       * #volatile
-       */
-      progress: '',
-      /**
-       * #volatile
-       */
-      error: undefined as unknown,
-      /**
-       * #volatile
-       */
-      loadingStoredData: false,
-    }))
+    .volatile(
+      (): {
+        rid: string | undefined
+        progress: string
+        error: unknown
+        loadingStoredData: boolean
+      } => ({
+        /**
+         * #volatile
+         */
+        rid: undefined,
+        /**
+         * #volatile
+         */
+        progress: '',
+        /**
+         * #volatile
+         */
+        error: undefined,
+        /**
+         * #volatile
+         */
+        loadingStoredData: false,
+      }),
+    )
 
     .views(self => ({
       /**
@@ -191,11 +198,15 @@ export default function stateModelFactory() {
         return self.connectedStructures
           .map(conn => {
             const proteinView = views.find(
-              (v: any) => v.id === conn.proteinViewId,
-            ) as any
+              (v: unknown) =>
+                (v as Record<string, unknown>).id === conn.proteinViewId,
+            )
             return proteinView ? { ...conn, proteinView } : undefined
           })
-          .filter((c): c is StructureConnection & { proteinView: any } => !!c)
+          .filter(
+            (c): c is StructureConnection & { proteinView: any } =>
+              c !== undefined,
+          )
       },
     }))
 

package/src/MsaViewPanel/pairwiseAlignment.ts

@@ -88,10 +88,11 @@ export function needlemanWunsch(
       const matchScore = getScore(seq1[i - 1]!, seq2[j - 1]!)
       const prevM = M[i - 1]![j - 1]!
       const prevIx = Ix[i - 1]![j - 1]!
+      const currentScore = M[i]![j]!
 
-      if (M[i]![j]! === prevM + matchScore) {
+      if (currentScore === prevM + matchScore) {
         currentMatrix = 'M'
-      } else if (M[i]![j]! === prevIx + matchScore) {
+      } else if (currentScore === prevIx + matchScore) {
         currentMatrix = 'Ix'
       } else {
         currentMatrix = 'Iy'
@@ -102,13 +103,17 @@ export function needlemanWunsch(
       alignedSeq1 = seq1[i - 1] + alignedSeq1
       alignedSeq2 = '-' + alignedSeq2
 
-      currentMatrix = Ix[i]![j]! === M[i - 1]![j]! + gapOpen ? 'M' : 'Ix'
+      const ixScore = Ix[i]![j]!
+      const mScore = M[i - 1]![j]! + gapOpen
+      currentMatrix = ixScore === mScore ? 'M' : 'Ix'
       i--
     } else if (j > 0) {
       alignedSeq1 = '-' + alignedSeq1
       alignedSeq2 = seq2[j - 1] + alignedSeq2
 
-      currentMatrix = Iy[i]![j]! === M[i]![j - 1]! + gapOpen ? 'M' : 'Iy'
+      const iyScore = Iy[i]![j]!
+      const mScore = M[i]![j - 1]! + gapOpen
+      currentMatrix = iyScore === mScore ? 'M' : 'Iy'
       j--
     } else {
       break

package/src/utils/blastCache.ts

@@ -40,11 +40,10 @@ function createCacheKey(
   blastProgram: string,
   transcriptId?: string,
 ) {
-  const seqKey = proteinSequence.slice(0, 100)
   if (transcriptId) {
-    return `${blastDatabase}:${blastProgram}:${transcriptId}:${seqKey}`
+    return `${blastDatabase}:${blastProgram}:${transcriptId}:${proteinSequence}`
   }
-  return `${blastDatabase}:${blastProgram}:${seqKey}`
+  return `${blastDatabase}:${blastProgram}:${proteinSequence}`
 }
 
 export async function getCachedBlastResult({

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.2.11'
+export const version = '2.3.5'