JAL-2233 reverted changes to Jmol logging levels

[jalview.git] / src / jalview / appletgui / AppletJmol.java

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 0379615..8374721 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -25,6 +25,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileParse;
+import jalview.io.StructureFile;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
@@ -179,10 +180,8 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     this.ap = ap;
     jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
-            new PDBEntry[]
-            { pdbentry }, new SequenceI[][]
-            { seq }, new String[][]
-            { chains }, protocol);
+            new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
+            new String[][] { chains }, protocol);
     jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
@@ -206,7 +205,7 @@ public class AppletJmol extends EmbmenuFrame implements
     String alreadyMapped = StructureSelectionManager
             .getStructureSelectionManager(ap.av.applet)
             .alreadyMappedToFile(pdbentry.getId());
-    MCview.PDBfile reader = null;
+    StructureFile reader = null;
     if (alreadyMapped != null)
     {
       reader = StructureSelectionManager.getStructureSelectionManager(
@@ -285,6 +284,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
     this.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent evt)
       {
         closeViewer();
@@ -347,7 +347,9 @@ public class AppletJmol extends EmbmenuFrame implements
           }
           if (freader == null)
           {
-            throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
+            throw new Exception(
+                    MessageManager
+                            .getString("exception.invalid_datasource_couldnt_obtain_reader"));
           }
           jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
                   freader);
@@ -415,6 +417,7 @@ public class AppletJmol extends EmbmenuFrame implements
     this.setVisible(false);
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == mappingMenuItem)
@@ -535,6 +538,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.setColourBySequence(itm == seqColour);
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == jmolColour)
@@ -553,6 +557,7 @@ public class AppletJmol extends EmbmenuFrame implements
     }
   }
 
+  @Override
   public void keyPressed(KeyEvent evt)
   {
     if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
@@ -564,10 +569,12 @@ public class AppletJmol extends EmbmenuFrame implements
 
   }
 
+  @Override
   public void keyTyped(KeyEvent evt)
   {
   }
 
+  @Override
   public void keyReleased(KeyEvent evt)
   {
   }
@@ -641,11 +648,13 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     Dimension currentSize = new Dimension();
 
+    @Override
     public void update(Graphics g)
     {
       paint(g);
     }
 
+    @Override
     public void paint(Graphics g)
     {
       currentSize = this.getSize();