jbrowse-plugin-msaview 2.6.1 → 2.6.2

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,24 +1,14 @@
 export default function LaunchMsaViewExtensionPointF(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, }) => {
+    pluginManager.addToExtensionPoint('LaunchView-MsaView', (args) => {
+        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,
@@ -29,5 +19,6 @@ export default function LaunchMsaViewExtensionPointF(pluginManager) {
                 querySeqName,
             },
         });
+        return args;
     });
 }

package/dist/MsaViewPanel/afterCreateAutoruns.js

@@ -116,13 +116,17 @@ export function autoLoadProteinDomains(self) {
         })();
     }
 }
+// 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) {
     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);
                     if (id) {
@@ -137,12 +141,7 @@ export function processInit(self) {
                     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({
@@ -160,12 +159,7 @@ export function processInit(self) {
                     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);
             }