61b5e11ec9bcc55bf7566ce4d176c7caff2bdf59
tdreszer
  Fri May 16 13:29:22 2014 -0700
Fixed setTimeouts (thanks Angie) and marked some code as possibly DEAD.
diff --git src/hg/js/alleles.js src/hg/js/alleles.js
index 2a81e7c..e702025 100644
--- src/hg/js/alleles.js
+++ src/hg/js/alleles.js
@@ -97,32 +97,33 @@
         }
     }
 
     function persistThroughUpdates()
     { // When an ajax update occurs, restore the non-ajax settings state
         
         // See if table was sorted previously
         if (persistSortColId !== '') {
     
             var col = $('table#alleles').find('TH#' + persistSortColId);
             if (col && col.length !== 0) {
                 var colIx = Number( $(col).attr('cellIndex') );
                 $(col).click();
                 if (persistSortReverse) {// click twice if reverse order!
                     persistSortReverse = false; // Needed so that it is set again
-                    setTimeout("$('table#alleles').find('TH#" + persistSortColId + 
-                                                                          "').click();", 50);
+                    setTimeout(function() { 
+                                    $('table#alleles').find('TH#' + persistSortColId).click(); 
+                                }, 50);
                 }
             }
         }
         
         // Make sure that sort command saves the coumn for persistence
         $('table#alleles').find('TH').click(function (e) { afterSort(this); });
         
         // Persist on lighlite as red
         if (hiliteId !== '')
             hiliteSpecial( hiliteId );
     }
 
     function propgateTitle(obj)
     { // Adds this objects title to all other objs with the same class
       // Relies upon a span and fixed width text
@@ -389,31 +390,31 @@
             var tripletButton = normed( $('input#'+sectionName+'_triplets') );
             if (tripletButton && $(tripletButton).val().indexOf('Show') === -1)
                 seqCharsPerPos = 3;
             seqPxPerPos = 7;
             var fullSeqHeader = normed( $(tbl).find('TH.seq') );
             if (fullSeqHeader) {
                 var seqLen = $(fullSeqHeader).text().length;
                 //if (seqCharsPerPos === 3)
                 //    seqLen /= 2;
                 seqPxPerPos = Math.round( $(fullSeqHeader).width() / (seqLen / seqCharsPerPos));
                 if ($.browser.msie) 
                     seqPxPerPos = $(fullSeqHeader).width() / (seqLen / seqCharsPerPos);
             }
             
             // Highlight variants in full sequence
-            setTimeout(alleles.delayedHilites(), 200);  // Delay till after page settles
+            setTimeout(alleles.delayedHilites, 200);  // Delay till after page settles
             
             // Want to sort on previos column if there was a sort before ajax update
             persistThroughUpdates();
         }
         
     };
 }()); // end & invocation of function that makes alleles
 
 // The following js depends upon the jQuery library
 $(document).ready(function()
 {
     // Gene Alleles table is sortable
     alleles.initialize();
     
     // This is really hgGene specific at this point...