Merge branch 'Release_2_8_3_Branch' of https://source.jalview.org/git/jalview into...

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 86ab536..04235be 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -20,28 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -73,6 +51,28 @@ import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 public class AppJmol extends StructureViewerBase
 {
   AppJmolBinding jmb;
@@ -184,7 +184,7 @@ public class AppJmol extends StructureViewerBase
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
-        closeViewer();
+        closeViewer(false);
       }
     });
     initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
@@ -406,7 +406,7 @@ public class AppJmol extends StructureViewerBase
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
-        closeViewer();
+        closeViewer(false);
       }
     });
 
@@ -602,8 +602,9 @@ public class AppJmol extends StructureViewerBase
     jmb.centerViewer(toshow);
   }
 
-  public void closeViewer()
+  public void closeViewer(boolean closeExternalViewer)
   {
+    // JMol does not use an external viewer
     jmb.closeViewer();
     setAlignmentPanel(null);
     _aps.clear();