X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=ed42ffa7c98761275a3e42a9015e8dc12e183c9e;hb=7f09e6ac5717bc78373c5d77f309831403e6ebf8;hp=6ebbf89425d532d017d9159a0fa05ac43f66ce7a;hpb=9ffbc78ef4639f680f304758c88d4e1d98c13859;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 6ebbf89..ed42ffa 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -47,6 +47,7 @@ import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
@@ -87,12 +88,20 @@ public abstract class StructureViewerBase extends GStructureViewer
     BySequence, ByChain, ChargeCysteine, ByViewer
   }
 
-  private static List<StructureViewerBase> svbs = new ArrayList<>();
+  /**
+   * Singleton list of all (open) instances of structureViewerBase
+   * TODO: JAL-3362 - review and adopt the swingJS-safe singleton pattern so each structure viewer base instance is kept to its own JalviewJS parent
+   */
+  private static List<JalviewStructureDisplayI> svbs = new ArrayList<>();
 
-  public static List<StructureViewerBase> getAllStructureViewerBases()
+  /**
+   * 
+   * @return list with all existing StructureViewers instance
+   */
+  public static List<JalviewStructureDisplayI> getAllStructureViewerBases()
   {
-    List<StructureViewerBase> goodSvbs = new ArrayList<>();
-    for (StructureViewerBase s : svbs)
+    List<JalviewStructureDisplayI> goodSvbs = new ArrayList<>();
+    for (JalviewStructureDisplayI s : svbs)
     {
       if (s != null && !goodSvbs.contains(s))
       {
@@ -196,6 +205,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     return _aps.contains(ap2.av.getSequenceSetId());
   }
 
+  @Override
   public boolean isUsedforaligment(AlignmentViewPanel ap2)
   {
 
@@ -1352,6 +1362,13 @@ public abstract class StructureViewerBase extends GStructureViewer
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     // jmb = null;
+    
+    try {
+      svbs.remove(this);
+    } catch (Throwable t)
+    {
+      Console.info("Unexpected exception when deregistering structure viewer",t);
+    }
     dispose();
   }