jbrowse-plugin-msaview 2.6.1 → 2.6.2

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.6.1";
+export declare const version = "2.6.2";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.6.1';
+export const version = '2.6.2';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.6.1",
+  "version": "2.6.2",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {

package/src/LaunchMsaViewExtensionPoint/index.ts

@@ -1,73 +1,56 @@
 import type PluginManager from '@jbrowse/core/PluginManager'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 
+interface LaunchMsaViewArgs {
+  session: AbstractSessionModel
+  data?: { msa: string; tree?: string }
+  msaFileLocation?: { uri: string }
+  msaIndexedLocation?: { uri: string }
+  msaName?: string
+  treeFileLocation?: { uri: string }
+  connectedViewId?: string
+  connectedFeature?: Record<string, unknown>
+  displayName?: string
+  colorSchemeName?: string
+  colWidth?: number
+  rowHeight?: number
+  treeAreaWidth?: number
+  treeWidth?: number
+  drawNodeBubbles?: boolean
+  labelsAlignRight?: boolean
+  showBranchLen?: boolean
+  querySeqName?: string
+  highlightColumns?: number[]
+}
+
 export default function LaunchMsaViewExtensionPointF(
   pluginManager: PluginManager,
 ) {
   pluginManager.addToExtensionPoint(
     'LaunchView-MsaView',
-    // @ts-expect-error
-    ({
-      session,
-      data,
-      msaFileLocation,
-      msaIndexedLocation,
-      msaName,
-      treeFileLocation,
-      connectedViewId,
-      connectedFeature,
-      displayName,
-      colorSchemeName,
-      colWidth,
-      rowHeight,
-      treeAreaWidth,
-      treeWidth,
-      drawNodeBubbles,
-      labelsAlignRight,
-      showBranchLen,
-      querySeqName,
-      highlightColumns,
-    }: {
-      session: AbstractSessionModel
-      data?: { msa: string; tree?: string }
-      msaFileLocation?: { uri: string }
-      msaIndexedLocation?: { uri: string }
-      msaName?: string
-      treeFileLocation?: { uri: string }
-      connectedViewId?: string
-      connectedFeature?: Record<string, unknown>
-      displayName?: string
-      colorSchemeName?: string
-      colWidth?: number
-      rowHeight?: number
-      treeAreaWidth?: number
-      treeWidth?: number
-      drawNodeBubbles?: boolean
-      labelsAlignRight?: boolean
-      showBranchLen?: boolean
-      querySeqName?: string
-      highlightColumns?: number[]
-    }) => {
+    (args: LaunchMsaViewArgs) => {
+      const {
+        session,
+        data,
+        msaFileLocation,
+        msaIndexedLocation,
+        msaName,
+        treeFileLocation,
+        querySeqName,
+        ...rest
+      } = args
+
       if (!data && !msaFileLocation && !msaIndexedLocation) {
         throw new Error(
           'No MSA data or file location provided when launching MSA view',
         )
       }
 
+      // all data sources flow through `init` so processInit is the single place
+      // that resolves them (AlphaFold detection, native filehandle loading, etc.)
       session.addView('MsaView', {
         type: 'MsaView',
-        displayName,
-        connectedViewId,
-        connectedFeature,
-        colorSchemeName,
-        colWidth,
-        rowHeight,
-        treeAreaWidth,
-        treeWidth,
-        drawNodeBubbles,
-        labelsAlignRight,
-        showBranchLen,
-        highlightColumns,
+        ...rest,
         init: {
           msaData: data?.msa,
           treeData: data?.tree,
@@ -78,6 +61,8 @@ export default function LaunchMsaViewExtensionPointF(
           querySeqName,
         },
       })
+
+      return args
     },
   )
 }

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -128,21 +128,25 @@ export function autoLoadProteinDomains(self: JBrowsePluginMsaViewModel) {
   }
 }
 
+// Resolve the declarative `init` launch contract once. Inline strings go straight
+// to the data model; URLs are handed to react-msaview's native filehandle loaders
+// (openLocation + progress + abort + CORS-proxy) rather than a hand-rolled fetch;
+// the bgzip name-indexed block is the one source with no native loader.
 export function processInit(self: JBrowsePluginMsaViewModel) {
   const { init } = self
   if (init) {
+    const {
+      msaData,
+      msaUrl,
+      msaIndexedLocation,
+      msaName,
+      treeData,
+      treeUrl,
+      querySeqName,
+    } = init
     void (async () => {
       try {
         self.setError(undefined)
-        const {
-          msaData,
-          msaUrl,
-          msaIndexedLocation,
-          msaName,
-          treeData,
-          treeUrl,
-          querySeqName,
-        } = init
 
         if (msaUrl) {
           const id = getUniprotIdFromAlphaFoldUrl(msaUrl)
@@ -151,7 +155,6 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
             self.setQuerySeqName('query')
           }
         }
-
         if (querySeqName) {
           self.setQuerySeqName(querySeqName)
         }
@@ -159,12 +162,7 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
         if (msaData) {
           self.setMSA(msaData)
         } else if (msaUrl) {
-          const response = await fetch(msaUrl)
-          if (!response.ok) {
-            throw new Error(`Failed to fetch MSA: ${response.status}`)
-          }
-          const data = await response.text()
-          self.setMSA(data)
+          self.setMSAFilehandle({ uri: msaUrl, locationType: 'UriLocation' })
         } else if (msaIndexedLocation && msaName) {
           const fasta = await fetchIndexedMsa({
             location: msaIndexedLocation,
@@ -182,12 +180,7 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
         if (treeData) {
           self.setTree(treeData)
         } else if (treeUrl) {
-          const response = await fetch(treeUrl)
-          if (!response.ok) {
-            throw new Error(`Failed to fetch tree: ${response.status}`)
-          }
-          const data = await response.text()
-          self.setTree(data)
+          self.setTreeFilehandle({ uri: treeUrl, locationType: 'UriLocation' })
         }
 
         self.setInit(undefined)

package/src/MsaViewPanel/types.ts

@@ -1,3 +1,6 @@
+// Declarative launch contract, resolved once by processInit. This is also a
+// cross-repo contract: jbrowse-plugin-protein3d builds an MsaView snapshot
+// directly with `init: { msaUrl }`, so these keys must stay stable.
 export interface MsaViewInitState {
   msaData?: string
   msaUrl?: string

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.6.1'
+export const version = '2.6.2'