JAL-4241 Fix annotation and feature alignment with selection

[jalview.git] / src / jalview / ws2 / actions / annotation / AlignCalcWorkerAdapter.java

diff --git a/src/jalview/ws2/actions/annotation/AlignCalcWorkerAdapter.java b/src/jalview/ws2/actions/annotation/AlignCalcWorkerAdapter.java
index 0905ea2..60d7f15 100644 (file)
--- a/src/jalview/ws2/actions/annotation/AlignCalcWorkerAdapter.java
+++ b/src/jalview/ws2/actions/annotation/AlignCalcWorkerAdapter.java
@@ -3,8 +3,6 @@ package jalview.ws2.actions.annotation;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
-import java.util.concurrent.CopyOnWriteArrayList;
-import java.util.function.Consumer;
 
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.api.AlignViewportI;
@@ -45,9 +43,9 @@ public class AlignCalcWorkerAdapter extends AlignCalcWorker implements PollableA
           ala.graphGroup += graphGroup;
         var newAnnot = alignViewport.getAlignment()
             .updateFromOrCopyAnnotation(ala);
-        if (ala.sequenceRef != null)
+        if (newAnnot.sequenceRef != null)
         {
-          ala.sequenceRef.addAlignmentAnnotation(newAnnot);
+          newAnnot.sequenceRef.addAlignmentAnnotation(newAnnot);
           newAnnot.adjustForAlignment();
           AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(
               newAnnot, newAnnot.label, newAnnot.getCalcId());
@@ -59,7 +57,7 @@ public class AlignCalcWorkerAdapter extends AlignCalcWorker implements PollableA
           AlignCalcWorkerAdapter.this,
           new AnnotationResult(
               annotations,
-              result.transferFeatures,
+              result.hasFeatures,
               result.featureColours,
               result.featureFilters));
     }
@@ -179,7 +177,7 @@ public class AlignCalcWorkerAdapter extends AlignCalcWorker implements PollableA
   }
 
   private WorkerListener listener = WorkerListener.NULL_LISTENER;
-  
+
   public void setWorkerListener(WorkerListener listener)
   {
     if (listener == null) listener = WorkerListener.NULL_LISTENER;