JAL-3551 pull up Close Viewer dialog to base class

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 0768c00..0610239 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -20,19 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.BrowserLauncher;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -49,6 +36,20 @@ import javax.swing.SwingUtilities;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.structure.StructureCommand;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
+
 public class AppJmol extends StructureViewerBase
 {
   // ms to wait for Jmol to load files
@@ -182,7 +183,10 @@ public class AppJmol extends StructureViewerBase
     useAlignmentPanelForColourbyseq(ap);
 
     alignAddedStructures = alignAdded;
-    useAlignmentPanelForSuperposition(ap);
+    if (pdbentrys.length > 1)
+    {
+      useAlignmentPanelForSuperposition(ap);
+    }
 
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
@@ -245,29 +249,12 @@ public class AppJmol extends StructureViewerBase
     {
       command = "";
     }
-    jmb.executeCommand(command, false);
-    jmb.executeCommand("set hoverDelay=0.1", false);
+    jmb.executeCommand(new StructureCommand(command), false);
+    jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
     jmb.setFinishedInit(true);
   }
 
   @Override
-  public void closeViewer(boolean closeExternalViewer)
-  {
-    // Jmol does not use an external viewer
-    if (jmb != null)
-    {
-      jmb.closeViewer();
-    }
-    setAlignmentPanel(null);
-    _aps.clear();
-    _alignwith.clear();
-    _colourwith.clear();
-    // TODO: check for memory leaks where instance isn't finalised because jmb
-    // holds a reference to the window
-    jmb = null;
-  }
-
-  @Override
   public void run()
   {
     _started = true;
@@ -323,7 +310,7 @@ public class AppJmol extends StructureViewerBase
       cmd.append("loadingJalviewdata=true\nload APPEND ");
       cmd.append(filesString);
       cmd.append("\nloadingJalviewdata=null");
-      final String command = cmd.toString();
+      final StructureCommand command = new StructureCommand(cmd.toString());
       lastnotify = jmb.getLoadNotifiesHandled();
 
       try
@@ -665,12 +652,6 @@ public class AppJmol extends StructureViewerBase
   }
 
   @Override
-  public String getStateInfo()
-  {
-    return jmb == null ? null : jmb.jmolViewer.getStateInfo();
-  }
-
-  @Override
   public ViewerType getViewerType()
   {
     return ViewerType.JMOL;