JAL-2233 less verbose logging for Jmol

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 8374721..264ac14 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -64,6 +64,8 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
+import org.jmol.util.Logger;
+
 public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
         KeyListener, ActionListener, ItemListener
@@ -269,6 +271,7 @@ public class AppletJmol extends EmbmenuFrame implements
       jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
               + "_jmol_", ap.av.applet.getDocumentBase(),
               ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
+      Logger.setLogLevel(Logger.LEVEL_WARN);
     } catch (Exception e)
     {
       System.err

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2ccf118..b1b5ce4 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -449,12 +449,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
       if (selectioncom.length() > 0)
       {
-        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; ");
         // 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);
       }
@@ -465,7 +465,7 @@ 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());

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index cef552f..65b4b96 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -124,8 +124,13 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     {
       try
       {
+        /*
+         * params -o (output to sysout) -i (no info logging, less verbose)
+         * -n (nodisplay) -x (exit when finished)
+         * see http://wiki.jmol.org/index.php/Jmol_Application
+         */
         viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
-                null, "-x -o -n", this);
+                null, "-x -o -n -i", this);
         // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
         viewer.setBooleanProperty("defaultStructureDSSP", true);
       } catch (ClassCastException x)

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index a1846bc..7929787 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -375,8 +375,11 @@ public class AppJmol extends StructureViewerBase
       scriptWindow.setVisible(false);
     }
 
-    jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
-            null);
+    /*
+     * -i for no info logging (less verbose)
+     */
+    jmb.allocateViewer(renderPanel, true, "", null, null, "-i",
+            scriptWindow, null);
     // jmb.newJmolPopup("Jmol");
     if (command == null)
     {