JAL-961 configure conservation worker from alignment viewport

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 681007e..a8bc268 100644 (file)
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -80,7 +80,7 @@ public class ConservationThread extends AlignCalcWorker implements
       ourAnnot.add(conservation);
       ourAnnot.add(quality);
       ourAnnots = ourAnnot;
-
+      ConsPercGaps = alignViewport.getConsPercGaps();
       // AlignViewport.UPDATING_CONSERVATION = true;
 
       if (alignment == null || (alWidth = alignment.getWidth()) < 0)