JAL-1588 refactoring prior to 'save Chimera project'

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

diff --git a/src/jalview/gui/ScriptWindow.java b/src/jalview/gui/ScriptWindow.java
index ff377f7..641efcb 100644 (file)
--- a/src/jalview/gui/ScriptWindow.java
+++ b/src/jalview/gui/ScriptWindow.java
@@ -1,34 +1,42 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
 import org.jmol.api.*;
 
+import jalview.jbgui.GStructureViewer;
+
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 import javax.swing.text.*;
+
 import java.util.Vector;
 
 import org.jmol.i18n.GT;
 import org.jmol.util.Logger;
 import org.jmol.util.CommandHistory;
 
+// TODO: this class is copied in from jmol 11.0.2 - upgrade to 12.0.2 ?
 public final class ScriptWindow extends JPanel implements ActionListener,
         EnterListener
 {
@@ -49,11 +57,11 @@ public final class ScriptWindow extends JPanel implements ActionListener,
 
   JmolViewer viewer;
 
-  AppJmol appJmol;
+  GStructureViewer appJmol;
 
   public ScriptWindow(AppJmol appJmol)
   {
-    this.viewer = appJmol.viewer;
+    this.viewer = appJmol.jmb.viewer;
     this.appJmol = appJmol;
 
     setLayout(new BorderLayout());
@@ -230,7 +238,7 @@ public final class ScriptWindow extends JPanel implements ActionListener,
       else
       {
         boolean isScriptExecuting = viewer.isScriptExecuting();
-        if (viewer.checkHalt(strCommand))
+        if (viewer.checkHalt(strCommand, true))
           strErrorMessage = (isScriptExecuting ? "string execution halted with "
                   + strCommand
                   : "no script was executing");
@@ -258,7 +266,7 @@ public final class ScriptWindow extends JPanel implements ActionListener,
     Object source = e.getSource();
     if (source == closeButton)
     {
-      appJmol.showConsole(false);
+      // appJmol.showConsole(false);
     }
     else if (source == runButton)
     {