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 b464c94..a577559 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -28,6 +28,7 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.AtomSpec;
@@ -56,7 +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
@@ -169,12 +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();
@@ -310,6 +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++)
       {
@@ -355,6 +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;
@@ -452,12 +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);
       }
@@ -468,7 +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());
@@ -552,6 +552,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     System.out.println("JMOL CREATE IMAGE");
   }
 
+  @Override
   public String createImage(String fileName, String type,
           Object textOrBytes, int quality)
   {
@@ -559,6 +560,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return null;
   }
 
+  @Override
   public String eval(String strEval)
   {
     // System.out.println(strEval);
@@ -569,11 +571,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   // End StructureListener
   // //////////////////////////
 
+  @Override
   public float[][] functionXY(String functionName, int x, int y)
   {
     return null;
   }
 
+  @Override
   public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
   {
     // TODO Auto-generated method stub
@@ -737,6 +741,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     if (atoms != null)
     {
+      if (resetLastRes.length() > 0)
+      {
+        viewer.evalStringQuiet(resetLastRes.toString());
+        resetLastRes.setLength(0);
+      }
       for (AtomSpec atom : atoms)
       {
         highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
@@ -768,17 +777,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
 
     jmolHistory(false);
-    // if (!pdbfile.equals(pdbentry.getFile()))
-    // return;
-    if (resetLastRes.length() > 0)
-    {
-      viewer.evalStringQuiet(resetLastRes.toString());
-    }
 
     StringBuilder cmd = new StringBuilder(64);
     cmd.append("select " + pdbResNum); // +modelNum
 
-    resetLastRes.setLength(0);
     resetLastRes.append("select " + pdbResNum); // +modelNum
 
     cmd.append(":");
@@ -1119,7 +1121,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       String fileName = modelfilenames[modelnum];
       boolean foundEntry = false;
-      MCview.PDBfile pdb = null;
+      StructureFile pdb = null;
       String pdbfile = null;
       // model was probably loaded inline - so check the pdb file hashcode
       if (loadedInline)
@@ -1142,7 +1144,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           {
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
                     pdbfile, AppletFormatAdapter.PASTE);
-            getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
+            getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
           }
@@ -1181,10 +1183,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         if (matches)
         {
           // add an entry for every chain in the model
-          for (int i = 0; i < pdb.chains.size(); i++)
+          for (int i = 0; i < pdb.getChains().size(); i++)
           {
-            String chid = new String(pdb.id + ":"
-                    + pdb.chains.elementAt(i).id);
+            String chid = new String(pdb.getId() + ":"
+                    + pdb.getChains().elementAt(i).id);
             chainFile.put(chid, fileName);
             chainNames.addElement(chid);
           }
@@ -1264,6 +1266,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   public abstract void sendConsoleMessage(String strStatus);
 
+  @Override
   public void setCallbackFunction(String callbackType,
           String callbackFunction)
   {