Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index c1c88c1..c01be4e 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -22,6 +22,7 @@ package jalview.viewmodel;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
+import jalview.analysis.Profile;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -700,7 +701,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   /**
    * results of alignment consensus analysis for visible portion of view
    */
-  protected Hashtable[] hconsensus = null;
+  protected Profile[] hconsensus = null;
 
   /**
    * results of cDNA complement consensus visible portion of view
@@ -734,7 +735,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public void setSequenceConsensusHash(Hashtable[] hconsensus)
+  public void setSequenceConsensusHash(Profile[] hconsensus)
   {
     this.hconsensus = hconsensus;
   }
@@ -746,7 +747,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public Hashtable[] getSequenceConsensusHash()
+  public Profile[] getSequenceConsensusHash()
   {
     return hconsensus;
   }
@@ -939,7 +940,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     groupConservation = null;
     hconsensus = null;
     hcomplementConsensus = null;
-    // TODO removed listeners from changeSupport?
+    // colour scheme may hold reference to consensus
+    globalColourScheme = null;
+    // TODO remove listeners from changeSupport?
     changeSupport = null;
     setAlignment(null);
   }