From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 11 Oct 2016 08:27:33 +0000 (+0100)
Subject: JAL-2233 reverted changes to Jmol logging levels
X-Git-Tag: Release_2_10_1~29
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9c66e390c2195d640a50bb645655c12158454f1e

JAL-2233 reverted changes to Jmol logging levels
---

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 264ac14..8374721 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -64,8 +64,6 @@ 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
@@ -271,7 +269,6 @@ 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 2f3464b..a577559 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -307,6 +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++)
       {
@@ -352,6 +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;
@@ -449,6 +451,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
       if (selectioncom.length() > 0)
       {
+        // 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; ");
diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 1800ef0..ca45d7b 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -124,12 +124,11 @@ 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)
+         * params -o (output to sysout) -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 -i", this);
+                null, "-x -o -n", 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 24604ed..021a004 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -381,10 +381,7 @@ public class AppJmol extends StructureViewerBase
       scriptWindow.setVisible(false);
     }
 
-    /*
-     * -i for no info logging (less verbose)
-     */
-    jmb.allocateViewer(renderPanel, true, "", null, null, "-i",
+    jmb.allocateViewer(renderPanel, true, "", null, null, "",
             scriptWindow, null);
     // jmb.newJmolPopup("Jmol");
     if (command == null)