protvista-uniprot 2.12.2 → 2.12.3

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "2.12.2",
+  "version": "2.12.3",
   "files": [
     "dist",
     "src"
@@ -29,24 +29,24 @@
     "data-loader": "^2.9.1",
     "file-saver": "^2.0.2",
     "lit-element": "^2.2.0",
-    "protvista-coloured-sequence": "3.8.13",
-    "protvista-datatable": "3.8.10",
-    "protvista-feature-adapter": "3.8.15",
-    "protvista-filter": "3.8.4",
-    "protvista-interpro-adapter": "3.8.14",
-    "protvista-interpro-track": "3.8.13",
-    "protvista-manager": "3.8.4",
-    "protvista-navigation": "3.8.10",
-    "protvista-proteomics-adapter": "3.8.15",
-    "protvista-sequence": "3.8.13",
-    "protvista-structure": "3.8.4",
-    "protvista-structure-adapter": "3.8.13",
-    "protvista-tooltip": "3.8.4",
-    "protvista-track": "3.8.16",
-    "protvista-variation": "3.8.13",
-    "protvista-variation-adapter": "3.8.13",
-    "protvista-variation-graph": "3.8.13",
-    "protvista-zoomable": "3.8.13",
+    "protvista-coloured-sequence": "3.8.22",
+    "protvista-datatable": "3.8.22",
+    "protvista-feature-adapter": "3.8.22",
+    "protvista-filter": "3.8.22",
+    "protvista-interpro-adapter": "3.8.22",
+    "protvista-interpro-track": "3.8.22",
+    "protvista-manager": "3.8.22",
+    "protvista-navigation": "3.8.22",
+    "protvista-proteomics-adapter": "3.8.22",
+    "protvista-sequence": "3.8.22",
+    "protvista-structure": "3.8.22",
+    "protvista-structure-adapter": "3.8.22",
+    "protvista-tooltip": "3.8.22",
+    "protvista-track": "3.8.22",
+    "protvista-variation": "3.8.22",
+    "protvista-variation-adapter": "3.8.22",
+    "protvista-variation-graph": "3.8.22",
+    "protvista-zoomable": "3.8.22",
     "timing-functions": "^2.0.1",
     "url-join": "^4.0.1"
   },

package/src/protvista-ptm-exchange.ts

@@ -91,9 +91,7 @@ const convertPtmExchangePtms = (
     console.log('PTM has no confidence score');
   } else if (confidenceScores.size > 1) {
     console.error(
-      `PTM has a mixture of confidence scores: ${Array.from(
-        confidenceScores
-      )}`
+      `PTM has a mixture of confidence scores: ${Array.from(confidenceScores)}`
     );
   } else {
     [confidenceScore] = confidenceScores;
@@ -101,22 +99,26 @@ const convertPtmExchangePtms = (
 
   const tooltip = `
   <h5>Description</h5><p>${phosphorylate(aa)}</p>
-  ${confidenceScore ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>` : ''}
+  ${
+    confidenceScore
+      ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>`
+      : ''
+  }
   ${
     evidences
       ? `<h5>Evidence</h5><ul>${evidences
-          .map(
-            (id) => {
-              const datasetID = id === 'Glue project' ? 'PXD012174' : id;
-              return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;
-              (<a href="https://www.ebi.ac.uk/pride/archive/projects/${id}" style="color:#FFF" target="_blank">PRIDE</a>)
+          .map((id) => {
+            const datasetID = id === 'Glue project' ? 'PXD012174' : id;
+            return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;
+              (<a href="https://proteomecentral.proteomexchange.org/dataset/${datasetID}" style="color:#FFF" target="_blank">ProteomeXchange</a>)
               </li>
-              ${id === 'Glue project' ?  
-              `<li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>`
-              : ''}
-              `
-            }
-          )
+              ${
+                id === 'Glue project'
+                  ? `<li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>`
+                  : ''
+              }
+              `;
+          })
           .join('')}</ul>`
       : ''
   }
@@ -139,7 +141,7 @@ export const transformData = (data: ProteomicsPtm) => {
 
     const absolutePositionToPtms: Record<number, { ptms: PTM[]; aa: string }> =
       {};
-  
+
     if (features) {
       for (const feature of features) {
         for (const ptm of feature.ptms) {
@@ -167,12 +169,12 @@ export const transformData = (data: ProteomicsPtm) => {
           }
         }
       }
-   
+
       return Object.entries(absolutePositionToPtms).map(
         ([absolutePosition, { ptms, aa }]) =>
           convertPtmExchangePtms(ptms, aa, +absolutePosition)
       );
-    } 
+    }
   }
-  return []; 
+  return [];
 };