Changeset 5812

Timestamp:

Jan 16, 2020, 8:35:19 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

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

Long REF and ALT sequnces are cut after 5 characters (and ... is appended). The full sequence is available as a tooltip.

Count and display number of SNV, Insertions and Deletions.

Location:

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

Files:

• view_variants.js (modified) (4 diffs)
• view_variants.jsp (modified) (1 diff)

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

@@ -22 +22 @@
     var snpData = response.snpData;
     
+    var numIns = 0;
+    var numDel = 0;
+    var numSnv = 0;
+    
     var html = '';
     for (var snpNo = 0; snpNo < snpData.length; snpNo++)
@@ -29 +33 @@
       var cosmicId = info['cosmic_ID'];
       var dbSnpId = info['dbsnp_ID'];
+      var type = info['TYPE'];
+      if (type == 'SNV') numSnv++;
+      else if (type == 'Insertion') numIns++;
+      else if (type == 'Deletion') numDel++;
       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">'+Strings.encodeTags(info['TYPE'])+'</td>';
-      html += '<td class="dottedleft">'+Strings.encodeTags(info['ncbiRefSeq'])+'</td>';
+      html += '<td class="dottedleft ref">'+vgt.getRefAndAlt(snp.ref, snp.alt)+'</td>';
+      html += '<td class="dottedleft">'+Strings.encodeTags(type)+'</td>';
+      html += '<td class="dottedleft">'+vgt.getGenes(info['ncbiRefSeq'])+'</td>';
       html += '<td class="dottedleft">'+vgt.getCosmicLink(cosmicId)+'</td>';
       html += '<td class="dottedleft">'+vgt.getDbSnpLink(dbSnpId)+'</td>';
@@ -40 +48 @@
     Doc.element('snp-list').innerHTML = html;
     Doc.show('snp-table', 'table');
-    Doc.element('snp-count').innerHTML = snpData.length + ' passed filter; ' + rba.VariantsRaw + ' raw variants';
+    Doc.element('snp-count').innerHTML = snpData.length + ' passed filter ('+
+      numSnv + ' SNV; ' + numIns + ' insertions; ' + numDel + ' deletions); ' +
+      rba.VariantsRaw + ' raw variants';
   }
   
@@ -54 +64 @@
     
     return Strings.encodeTags(list.join(', '));
+  }
+  
+  vgt.getGenes = function(genes)
+  {
+    if (!genes) return '';
+    return Strings.encodeTags(genes.split(',').join(', '));
+  }
+  
+  vgt.getRefAndAlt = function(ref, alt)
+  {
+    if (ref.length > 6) ref = '<span title="'+ref+'">'+ref.substring(0, 5)+'...</span>';
+    if (alt.length > 6) alt = '<span title="'+alt+'">'+alt.substring(0, 5)+'...</span>';
+    return ref + ' › ' + alt;
   }
   

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

@@ -59 +59 @@
 {
   text-align: center;
+  white-space: nowrap;
 }
 </style>