X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=2447a2f7402f0642d862d481368b94582ea172ac;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=217d2b1c5f89b5b641e38e5c31120d100b1587f1;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 217d2b1..2447a2f 100644
--- 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;
@@ -184,8 +184,7 @@ 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 +233,6 @@ public class AppJmol extends StructureViewerBase
     openNewJmol(ap, alignAdded, pe, seqs);
   }
 
-
   void initJmol(String command)
   {
     jmb.setFinishedInit(false);
@@ -309,10 +307,10 @@ 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 +331,11 @@ 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 +351,7 @@ 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 +434,8 @@ 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 +447,7 @@ 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());
@@ -523,7 +522,8 @@ 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);