factored out reference to parent alignFrame (so all views can be closed whilst a...

[jalview.git] / src / jalview / ws / MsaWSThread.java

diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 0dedce2..3be0c56 100644 (file)
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -622,7 +622,7 @@ class MsaWSThread
         results[j] = null;
       }
     }
-    Object[] newview = input.getUpdatedView(results, orders, '-');
+    Object[] newview = input.getUpdatedView(results, orders, getGapChar());
     // trash references to original result data
     for (int j = 0; j < jobs.length; j++)
     {
@@ -647,10 +647,9 @@ class MsaWSThread
                                      AlignFrame.DEFAULT_WIDTH,
                                      AlignFrame.DEFAULT_HEIGHT);
 
-      // >>>This is a fix for the moment, until a better solution is
-      // found!!<<<
+      // initialise with same renderer settings as in parent alignframe.
       af.getFeatureRenderer().transferSettings(
-          alignFrame.getFeatureRenderer());
+          this.featureSettings);
       // update orders
       if (alorders.size() > 0)
       {
@@ -714,7 +713,6 @@ class MsaWSThread
     }
   }
 
-
   public boolean canMergeResults()
   {
     return false;