npm - jbrowse-plugin-protein3d - Versions diffs - 0.0.3 → 0.0.5 - Mend

jbrowse-plugin-protein3d 0.0.3 → 0.0.5

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 (196) hide show

package/dist/ProteinView/highlightResidue.js CHANGED Viewed

@@ -6,8 +6,8 @@ export default function highlightResidue({ structure, selectedResidue, plugin, }
         selectedResidue: selectedResidue + 1,
     });
     const loci = StructureSelection.toLociWithSourceUnits(sel);
-    plugin?.managers.interactivity.lociHighlights.clearHighlights();
-    plugin?.managers.interactivity.lociHighlights.highlight({
+    plugin.managers.interactivity.lociHighlights.clearHighlights();
+    plugin.managers.interactivity.lociHighlights.highlight({
         loci,
     });
 }

package/dist/ProteinView/highlightResidue.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"highlightResidue.js","sourceRoot":"","sources":["../../src/ProteinView/highlightResidue.ts"],"names":[],"mappings":"AACA,OAAO,EAAa,kBAAkB,EAAE,MAAM,iCAAiC,CAAA;AAC/E,OAAO,EAAE,4BAA4B,EAAE,MAAM,QAAQ,CAAA;AAErD,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,EACvC,SAAS,EACT,eAAe,EACf,MAAM,GAKP;IACC,MAAM,GAAG,GAAG,4BAA4B,CAAC;QACvC,SAAS;QACT,eAAe,EAAE,eAAe,GAAG,CAAC;KACrC,CAAC,CAAA;IACF,MAAM,IAAI,GAAG,kBAAkB,CAAC,qBAAqB,CAAC,GAAG,CAAC,CAAA;IAC1D,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAC,cAAc,CAAC,eAAe,EAAE,CAAA;IAC9D,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAC,cAAc,CAAC,SAAS,CAAC;QACrD,IAAI;KACL,CAAC,CAAA;AACJ,CAAC"}

package/dist/ProteinView/launchRemotePairwiseAlignment.d.ts CHANGED Viewed

@@ -4,11 +4,8 @@ export declare function launchPairwiseAlignment({ algorithm, seq1, seq2, onProgr
     seq2: string;
     onProgress: (arg: string) => void;
 }): Promise<{
-    alignment: {
+    pairwiseAlignment: {
         consensus: string;
-        alns: {
-            id: any;
-            seq: any;
-        }[];
+        alns: [import("clustal-js").Row, import("clustal-js").Row];
     };
 }>;

package/dist/ProteinView/launchRemotePairwiseAlignment.js CHANGED Viewed

@@ -17,7 +17,7 @@ async function runEmbossMatcher({ seq1, seq2, onProgress, }) {
     });
     const ret = await textfetch(`${base}/emboss_matcher/result/${jobId}/aln`);
     return {
-        alignment: parsePairwise(ret
+        pairwiseAlignment: parsePairwise(ret
             .split('\n')
             .filter(line => !line.startsWith('#'))
             .join('\n')),
@@ -39,22 +39,26 @@ async function runEmbossNeedle({ seq1, seq2, onProgress, }) {
     });
     const ret = await textfetch(`${base}/emboss_needle/result/${jobId}/aln`);
     return {
-        alignment: parsePairwise(ret
+        pairwiseAlignment: parsePairwise(ret
             .split('\n')
             .filter(line => !line.startsWith('#'))
             .join('\n')),
     };
 }
 async function wait({ onProgress, jobId, algorithm, }) {
+    // eslint-disable-next-line  @typescript-eslint/no-unnecessary-condition
     while (true) {
         for (let i = 0; i < 10; i++) {
             await timeout(1000);
-            onProgress(`Re-checking alignment to PDB seq1,seq2 in... ${10 - i}`);
+            onProgress(`Re-checking pairwiseAlignment to PDB seq1,seq2 in... ${10 - i}`);
         }
         const result = await textfetch(`${base}/${algorithm}/status/${jobId}`);
         if (result === 'FINISHED') {
             break;
         }
+        else if (result.includes('FAILED')) {
+            throw new Error('Remote returned FAILED');
+        }
     }
 }
 export async function launchPairwiseAlignment({ algorithm, seq1, seq2, onProgress, }) {

package/dist/ProteinView/launchRemotePairwiseAlignment.js.map CHANGED Viewed

	@@ -1 +1 @@
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