X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAbstractJabaCalcWorker.java;h=2d9137790fb8ffe37b1f6eaa35ae92fd182c87a0;hb=53e0350c1c4464442938e4bace4e85bdbca665be;hp=5961fc3831384f7f20279ab65b470c88eada63d4;hpb=944fb0771776aeb297264fca9e10a3624695831f;p=jalview.git

diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index 5961fc3..2d91377 100644
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -347,6 +347,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
           jalview.bin.Cache.log.debug("Updating result annotation from Job "
                   + rslt + " at " + service.getUri());
           updateResultAnnotation(true);
+          ap.sortAnnotations(false);
           ap.adjustAnnotationHeight();
         }
       }
@@ -392,7 +393,8 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
         {
           guiProgress.setProgressBar("", progressId);
         }
-        ap.paintAlignment(true);
+        // TODO: may not need to paintAlignment again !
+        ap.paintAlignment(false, false);
       }
       if (msg.length() > 0)
       {
@@ -602,7 +604,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
   protected boolean checkDone()
   {
     calcMan.notifyStart(this);
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     while (!calcMan.notifyWorking(this))
     {
       if (calcMan.isWorking(this))
@@ -613,7 +615,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
       {
         if (ap != null)
         {
-          ap.paintAlignment(false);
+          ap.paintAlignment(false, false);
         }
 
         Thread.sleep(200);