From a53974449027202e8f6985f5191f0efbecd5342c Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 23 Mar 2023 14:51:32 +0000
Subject: [PATCH] JAL-4155 Viewport holds a reference to its
 AlignmentViewPanel - getter on gui.AlignViewport casts
 interface to gui.AlignmentPanel

---
 src/jalview/gui/AlignViewport.java           |   33 ++++++++++----------------
 src/jalview/gui/AlignmentPanel.java          |    1 +
 src/jalview/viewmodel/AlignmentViewport.java |   19 +++++++++++++++
 3 files changed, 32 insertions(+), 21 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2d82579..79a16ba 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -529,6 +529,16 @@ public class AlignViewport extends AlignmentViewport
                     this);
   }
 
+  
+  public boolean getSortByTree()
+  {
+    return sortByTree;
+  }
+
+  public void setSortByTree(boolean sort)
+  {
+    sortByTree = sort;
+  }
   /**
    * return the alignPanel containing the given viewport. Use this to get the
    * components currently handling the given viewport.
@@ -537,30 +547,11 @@ public class AlignViewport extends AlignmentViewport
    * @return null or an alignPanel guaranteed to have non-null alignFrame
    *         reference
    */
+  
   public AlignmentPanel getAlignPanel()
   {
-    AlignmentPanel[] aps = PaintRefresher
-            .getAssociatedPanels(this.getSequenceSetId());
-    for (int p = 0; aps != null && p < aps.length; p++)
-    {
-      if (aps[p].av == this)
-      {
-        return aps[p];
-      }
-    }
-    return null;
-  }
-
-  public boolean getSortByTree()
-  {
-    return sortByTree;
+    return (AlignmentPanel) alignPanel;
   }
-
-  public void setSortByTree(boolean sort)
-  {
-    sortByTree = sort;
-  }
-
   /**
    * Returns the (Desktop) instance of the StructureSelectionManager
    */
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index fd53faf..d90164f 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -128,6 +128,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // setBackground(Color.white); // BH 2019
     alignFrame = af;
     this.av = av;
+    av.setAlignPanel(this);
     setSeqPanel(new SeqPanel(av, this));
     setIdPanel(new IdPanel(av, this));
 
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 0e3bb9e..2b4074e 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -138,6 +138,24 @@ public abstract class AlignmentViewport
     ranges = new ViewportRanges(al);
   }
 
+  protected AlignmentViewPanel alignPanel=null;
+  public void setAlignPanel(AlignmentViewPanel ap)
+  {
+    alignPanel = ap;
+  }
+  /**
+   * return the AlignmentViewPanel containing the given viewport. Use this to get the
+   * components currently handling the given viewport.
+   * 
+   * @param av
+   * @return null or an alignPanel guaranteed to have non-null alignFrame
+   *         reference
+   */
+  
+  public AlignmentViewPanel getAlignPanel()
+  {
+    return alignPanel;
+  }
   /**
    * @param name
    * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
@@ -1027,6 +1045,7 @@ public abstract class AlignmentViewport
      * defensively null out references to large objects in case
      * this object is not garbage collected (as if!)
      */
+    alignPanel=null;
     consensus = null;
     complementConsensus = null;
     strucConsensus = null;
-- 
1.7.10.2