X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=8d83e75300f84e7cf0cb6a59b01ea31b40d24a27;hb=9ae61a06b581ffba65614a2f08acc36e7f7685e7;hp=874bfd30d36257f4a3e00303f065c8183e542206;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 874bfd3..8d83e75 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -30,7 +30,6 @@ import jalview.ext.jmol.JmolCommands;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
 
@@ -220,21 +219,22 @@ public class MouseOverStructureListener extends JSFunctionExec
 
       // Form a colour command from the given alignment panel for each distinct
       // structure
-      ArrayList<String[]> ccomands = new ArrayList<String[]>();
-      ArrayList<String> pdbfn = new ArrayList<String>();
-      StructureMappingcommandSet[] colcommands = JmolCommands
-              .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
+      ArrayList<String[]> ccomands = new ArrayList<>();
+      ArrayList<String> pdbfn = new ArrayList<>();
+      String[] colcommands = new JmolCommands()
+              .colourBySequence(ssm, modelSet, sequence, sr,
                       (AlignmentViewPanel) source);
       if (colcommands == null)
       {
         return;
       }
       int sz = 0;
-      for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      // for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      for (String command : colcommands)
       {
-        sz += ccset.commands.length;
-        ccomands.add(ccset.commands);
-        pdbfn.add(ccset.mapping);
+        // sz += ccset.commands.length;
+        // ccomands.add(command); // ccset.commands);
+        // pdbfn.add(ccset.mapping);
       }
 
       String mclass, mhandle;
@@ -299,13 +299,6 @@ public class MouseOverStructureListener extends JSFunctionExec
   }
 
   @Override
-  public void finalize() throws Throwable
-  {
-    jvlite = null;
-    super.finalize();
-  }
-
-  @Override
   public void releaseReferences(Object svl)
   {