JAL-2233 reverted changes to Jmol logging levels

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 3f0847b..a577559 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -57,7 +57,6 @@ import org.jmol.api.JmolStatusListener;
 import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
 import org.jmol.script.T;
-import org.jmol.viewer.JC;
 import org.jmol.viewer.Viewer;
 
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
@@ -170,12 +169,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   public void closeViewer()
   {
-    viewer.acm.setModeMouse(JC.MOUSE_NONE);
     // remove listeners for all structures in viewer
     getSsm().removeStructureViewerListener(this, this.getPdbFile());
-    // and shut down jmol
-    viewer.evalStringQuiet("zap");
-    viewer.setJmolStatusListener(null);
+    viewer.dispose();
     lastCommand = null;
     viewer = null;
     releaseUIResources();
@@ -311,6 +307,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
        * 'matched' array will hold 'true' for visible alignment columns where
        * all sequences have a residue with a mapping to the PDB structure
        */
+      // TODO could use a BitSet for matched
       boolean matched[] = new boolean[alignment.getWidth()];
       for (int m = 0; m < matched.length; m++)
       {
@@ -356,6 +353,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
        * generate select statements to select regions to superimpose structures
        */
       {
+        // TODO extract method to construct selection statements
         for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
         {
           String chainCd = ":" + structures[pdbfnum].chain;
@@ -453,12 +451,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
       if (selectioncom.length() > 0)
       {
-        System.out.println("Select regions:\n" + selectioncom.toString());
+        // TODO is performing selectioncom redundant here? is done later on
+        // System.out.println("Select regions:\n" + selectioncom.toString());
         evalStateCommand("select *; cartoons off; backbone; select ("
                 + selectioncom.toString() + "); cartoons; ");
         // selcom.append("; ribbons; ");
         String cmdString = command.toString();
-        System.out.println("Superimpose command(s):\n" + cmdString);
+        // System.out.println("Superimpose command(s):\n" + cmdString);
 
         evalStateCommand(cmdString);
       }
@@ -469,7 +468,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       {
         selectioncom.setLength(selectioncom.length() - 1);
       }
-      System.out.println("Select regions:\n" + selectioncom.toString());
+      // System.out.println("Select regions:\n" + selectioncom.toString());
       evalStateCommand("select *; cartoons off; backbone; select ("
               + selectioncom.toString() + "); cartoons; ");
       // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());