From 173f77ac7161e8866ddfe6b5689d61a83f459cfc Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 14 Sep 2017 10:05:43 +0100
Subject: [PATCH] JAL-2727 null more fields in AlignmentViewport.dispose();
 pull up currentTree

---
 src/jalview/api/AlignViewportI.java          |    5 +++++
 src/jalview/appletgui/AlignViewport.java     |   13 -------------
 src/jalview/gui/AlignViewport.java           |   24 ------------------------
 src/jalview/gui/Jalview2XML.java             |    4 ++--
 src/jalview/viewmodel/AlignmentViewport.java |   17 +++++++++++++++++
 5 files changed, 24 insertions(+), 39 deletions(-)

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9e6d1c0..248bae2 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,6 +21,7 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -494,4 +495,8 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   void setProteinFontAsCdna(boolean b);
+
+  public abstract TreeModel getCurrentTree();
+
+  public abstract void setCurrentTree(TreeModel tree);
 }
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index b07666e..c83f93f 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,7 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
@@ -54,8 +53,6 @@ public class AlignViewport extends AlignmentViewport
 
   boolean validCharWidth = true;
 
-  TreeModel currentTree = null;
-
   public jalview.bin.JalviewLite applet;
 
   boolean MAC = false;
@@ -274,16 +271,6 @@ public class AlignViewport extends AlignmentViewport
     ranges.setEndSeq(height / getCharHeight());
   }
 
-  public void setCurrentTree(TreeModel tree)
-  {
-    currentTree = tree;
-  }
-
-  public TreeModel getCurrentTree()
-  {
-    return currentTree;
-  }
-
   boolean centreColumnLabels;
 
   public boolean getCentreColumnLabels()
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index c22a37d..90271c8 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -76,8 +76,6 @@ public class AlignViewport extends AlignmentViewport
 {
   Font font;
 
-  TreeModel currentTree = null;
-
   boolean cursorMode = false;
 
   boolean antiAlias = false;
@@ -448,27 +446,6 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param tree
-   *          DOCUMENT ME!
-   */
-  public void setCurrentTree(TreeModel tree)
-  {
-    currentTree = tree;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public TreeModel getCurrentTree()
-  {
-    return currentTree;
-  }
-
-  /**
    * returns the visible column regions of the alignment
    * 
    * @param selectedRegionOnly
@@ -1110,5 +1087,4 @@ public class AlignViewport extends AlignmentViewport
     }
     fr.setTransparency(featureSettings.getTransparency());
   }
-
 }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1658f0f88..4fffe6f 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1084,7 +1084,7 @@ public class Jalview2XML
 
     // SAVE TREES
     // /////////////////////////////////
-    if (!storeDS && av.currentTree != null)
+    if (!storeDS && av.getCurrentTree() != null)
     {
       // FIND ANY ASSOCIATED TREES
       // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
@@ -1102,7 +1102,7 @@ public class Jalview2XML
             {
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
-              tree.setCurrentTree((av.currentTree == tp.getTree()));
+              tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
               tree.setNewick(tp.getTree().print());
               tree.setThreshold(tp.treeCanvas.threshold);
 
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a8afe9a..8e949a5 100644
--- 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;
@@ -955,6 +956,8 @@ public abstract class AlignmentViewport
     residueShading = null; // may hold a reference to Consensus
     changeSupport = null;
     ranges = null;
+    currentTree = null;
+    selectionGroup = null;
     setAlignment(null);
   }
 
@@ -2879,6 +2882,8 @@ public abstract class AlignmentViewport
    */
   private SearchResultsI searchResults = null;
 
+  protected TreeModel currentTree = null;
+
   @Override
   public boolean hasSearchResults()
   {
@@ -2937,4 +2942,16 @@ public abstract class AlignmentViewport
             + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
     return sq;
   }
+
+  @Override
+  public void setCurrentTree(TreeModel tree)
+  {
+    currentTree = tree;
+  }
+
+  @Override
+  public TreeModel getCurrentTree()
+  {
+    return currentTree;
+  }
 }
-- 
1.7.10.2