X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=0afa711f452042622c925b8319f7db9bd50696f1;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=54b0191169f79e21eebc431d55d75c3dbf5efc9c;hpb=106a3890f956e2aa7780b2985f4326655912a558;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 54b0191..0afa711 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -21,6 +21,7 @@
 package jalview.workers;
 
 import jalview.analysis.Conservation;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -95,9 +96,10 @@ public class ConservationThread extends AlignCalcWorker
       }
       try
       {
+        // TODO - TDI is there a conservation measure ?
         cons = Conservation.calculateConservation("All",
                 alignment.getSequences(), 0, alWidth - 1, false,
-                ConsPercGaps, quality != null);
+                ConsPercGaps, quality != null, alignViewport.is3di() ? ScoreModels.getInstance().getFOLDSEEK3DI():ScoreModels.getInstance().getDefaultModel(true));
       } catch (IndexOutOfBoundsException x)
       {
         // probable race condition. just finish and return without any fuss.