Merge branch 'bug/JAL-2727closeAllFreeMemory' into develop

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index b260cab..fdad0ce 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.TreeModel;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -79,7 +80,7 @@ import java.util.Map;
 public abstract class AlignmentViewport
         implements AlignViewportI, CommandListener, VamsasSource
 {
-  final protected ViewportRanges ranges;
+  protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
 
@@ -947,11 +948,15 @@ public abstract class AlignmentViewport
     groupConsensus = null;
     groupConservation = null;
     hconsensus = null;
+    hconservation = null;
     hcomplementConsensus = null;
-    // colour scheme may hold reference to consensus
-    residueShading = null;
-    // TODO remove listeners from changeSupport?
+    gapcounts = null;
+    calculator = null;
+    residueShading = null; // may hold a reference to Consensus
     changeSupport = null;
+    ranges = null;
+    currentTree = null;
+    selectionGroup = null;
     setAlignment(null);
   }
 
@@ -2869,6 +2874,8 @@ public abstract class AlignmentViewport
    */
   private SearchResultsI searchResults = null;
 
+  protected TreeModel currentTree = null;
+
   @Override
   public boolean hasSearchResults()
   {
@@ -2927,4 +2934,16 @@ public abstract class AlignmentViewport
             + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
     return sq;
   }
+
+  @Override
+  public void setCurrentTree(TreeModel tree)
+  {
+    currentTree = tree;
+  }
+
+  @Override
+  public TreeModel getCurrentTree()
+  {
+    return currentTree;
+  }
 }