Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / gui / AppJmol.java

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 217d2b1..0c36745 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -38,7 +38,7 @@ import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
 import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
@@ -52,7 +52,6 @@ import jalview.util.BrowserLauncher;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-
 public class AppJmol extends StructureViewerBase
 {
   // ms to wait for Jmol to load files
@@ -106,7 +105,6 @@ public class AppJmol extends StructureViewerBase
               .toArray(new SequenceI[sequencesForPdb.size()]);
       i++;
     }
-
     // TODO: check if protocol is needed to be set, and if chains are
     // autodiscovered.
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
@@ -134,7 +132,6 @@ public class AppJmol extends StructureViewerBase
       seqColour.setSelected(true);
       viewerColour.setSelected(false);
     }
-
     this.setBounds(viewerModel.getX(), viewerModel.getY(),
             viewerModel.getWidth(), viewerModel.getHeight());
     setViewId(viewid);
@@ -159,6 +156,7 @@ public class AppJmol extends StructureViewerBase
   {
     super.initMenus();
 
+
     viewerColour
             .setText(MessageManager.getString("label.colour_with_jmol"));
     viewerColour.setToolTipText(MessageManager
@@ -184,8 +182,7 @@ public class AppJmol extends StructureViewerBase
   }
 
   private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
-          PDBEntry[] pdbentrys,
-          SequenceI[][] seqs)
+          PDBEntry[] pdbentrys, SequenceI[][] seqs)
   {
     setProgressIndicator(ap.alignFrame);
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
@@ -234,7 +231,6 @@ public class AppJmol extends StructureViewerBase
     openNewJmol(ap, alignAdded, pe, seqs);
   }
 
-
   void initJmol(String command)
   {
     jmb.setFinishedInit(false);
@@ -309,10 +305,10 @@ public class AppJmol extends StructureViewerBase
       } catch (OutOfMemoryError oomerror)
       {
         new OOMWarning("When trying to open the Jmol viewer!", oomerror);
-        Cache.log.debug("File locations are " + filesString);
+        Console.debug("File locations are " + filesString);
       } catch (Exception ex)
       {
-        Cache.log.error("Couldn't open Jmol viewer!", ex);
+        Console.error("Couldn't open Jmol viewer!", ex);
         ex.printStackTrace();
         return;
       }
@@ -333,11 +329,11 @@ public class AppJmol extends StructureViewerBase
       {
         new OOMWarning("When trying to add structures to the Jmol viewer!",
                 oomerror);
-        Cache.log.debug("File locations are " + filesString);
+        Console.debug("File locations are " + filesString);
         return;
       } catch (Exception ex)
       {
-        Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+        Console.error("Couldn't add files to Jmol viewer!", ex);
         ex.printStackTrace();
         return;
       }
@@ -353,7 +349,7 @@ public class AppJmol extends StructureViewerBase
     {
       try
       {
-        Cache.log.debug("Waiting around for jmb notify.");
+        Console.debug("Waiting around for jmb notify.");
         waitTotal += waitFor;
 
         // Thread.sleep() throws an exception in JS
@@ -436,7 +432,8 @@ public class AppJmol extends StructureViewerBase
         jmb.jmolViewer.renderScreenImage(g, width, height);
       }
     };
-    String view = MessageManager.getString("action.view").toLowerCase(Locale.ROOT);
+    String view = MessageManager.getString("action.view")
+            .toLowerCase(Locale.ROOT);
     ImageExporter exporter = new ImageExporter(writer,
             getProgressIndicator(), type, getTitle());
     exporter.doExport(null, this, width, height, view);
@@ -448,7 +445,7 @@ public class AppJmol extends StructureViewerBase
     try
     {
       BrowserLauncher // BH 2018
-              .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
+              .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/");
     } catch (Exception ex)
     {
       System.err.println("Show Jmol help failed with: " + ex.getMessage());
@@ -458,6 +455,7 @@ public class AppJmol extends StructureViewerBase
   @Override
   public void showConsole(boolean showConsole)
   {
+
     if (showConsole)
     {
       if (splitPane == null)
@@ -523,7 +521,8 @@ public class AppJmol extends StructureViewerBase
           }
         }
       }
-      else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit())
+      else if (jmb == null || jmb.jmolViewer == null
+              || !jmb.isFinishedInit())
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);