Changeset 5805

Timestamp:

Jan 9, 2020, 9:49:48 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1221: Display more information in the Variant summary dialog

Added TYPE and dbSNP fields and changed the Gene field to use ncbiRefSeq instead of ANN.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/analysis/view_variants.js (modified) (2 diffs)
• resources/analysis/view_variants.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/VariantCallingServlet.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/resources/analysis/view_variants.js

@@ -28 +28 @@
       var info = snp.info;
       var cosmicId = info['cosmic_ID'];
+      var dbSnpId = info['dbsnp_ID'];
       html += '<tr class="snp highlight">';
       html += '<td>'+Strings.encodeTags(snp.chromosome+':'+snp.position)+'</td>';
       html += '<td class="dottedleft ref">'+Strings.encodeTags(snp.ref+' › '+snp.alt)+'</td>';
-      html += '<td class="dottedleft">'+vgt.getAnnValues(info, 'Gene_Name')+'</td>';
+      html += '<td class="dottedleft">'+Strings.encodeTags(info['TYPE'])+'</td>';
+      html += '<td class="dottedleft">'+Strings.encodeTags(info['ncbiRefSeq'])+'</td>';
       html += '<td class="dottedleft">'+vgt.getCosmicLink(cosmicId)+'</td>';
+      html += '<td class="dottedleft">'+vgt.getDbSnpLink(dbSnpId)+'</td>';
       html += '</tr>';
     }
@@ -70 +73 @@
   }
   
+  vgt.getDbSnpLink = function(rsId)
+  {
+    if (!rsId) return '';
+
+    var tmp = rsId.split(',');
+    var links = [];
+    for (var i = 0; i < tmp.length; i++)
+    {
+      var link = '<a target="_blank" title="View in dbSNP (new window)"';
+      link += ' href="https://www.ncbi.nlm.nih.gov/snp/'+encodeURIComponent(tmp[i])+'">';
+      link += Strings.encodeTags(tmp[i])+'</a>';
+      
+      links[i] = link;
+    }
+    return links.join(', ');
+  }
+  
   return vgt;
 }();

extensions/net.sf.basedb.reggie/trunk/resources/analysis/view_variants.jsp

@@ -94 +94 @@
       <th>Location</th>
       <th class="dottedleft ref">Ref › Alt</th>
+      <th class="dottedleft">Type</th>
       <th class="dottedleft">Gene</th>
       <th class="dottedleft">Cosmic ID</th>
+      <th class="dottedleft">dbSNP ID</th>
     </tr>
     <tbody id="snp-list"></tbody>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/VariantCallingServlet.java

@@ -217 +217 @@
           parser.setUseLineNoAsId(true);
           parser.setInfoFactory(new VariantCallingInfoFactory(
-              Arrays.asList("cosmic_ID"),
-              Arrays.asList("Gene_Name")
+              Arrays.asList("TYPE", "ncbiRefSeq", "cosmic_ID", "dbsnp_ID"),
+              null
               ));
           vcfIn = vcf.getDownloadStream(0);