X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScriptWindow.java;h=972e5ef27a7df1b14da29fc3df0b993ca01aecd0;hb=cb7bef47fe49963716fc33285fd4fb733ac95933;hp=00b724e3bd7419b1f63cfce5b4354df8d018946c;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/gui/ScriptWindow.java b/src/jalview/gui/ScriptWindow.java
index 00b724e..972e5ef 100644
--- a/src/jalview/gui/ScriptWindow.java
+++ b/src/jalview/gui/ScriptWindow.java
@@ -1,35 +1,42 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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
 {
@@ -50,11 +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());
@@ -231,7 +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");
@@ -259,7 +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)
     {
@@ -417,8 +424,8 @@ class ConsoleTextPane extends JTextPane
   /**
    * Recall command history.
    * 
-   * @param up -
-   *                history up or down
+   * @param up
+   *          - history up or down
    */
   void recallCommand(boolean up)
   {
@@ -499,12 +506,14 @@ class ConsoleDocument extends DefaultStyledDocument
   }
 
   Position positionBeforePrompt; // starts at 0, so first time isn't tracked
-                                  // (at least on Mac OS X)
+
+  // (at least on Mac OS X)
 
   Position positionAfterPrompt; // immediately after $, so this will track
 
   int offsetAfterPrompt; // only still needed for the insertString override and
-                          // replaceCommand
+
+  // replaceCommand
 
   /**
    * Removes all content of the script window, and add a new prompt.
@@ -700,9 +709,9 @@ class ConsoleDocument extends DefaultStyledDocument
    * Replaces current command on script.
    * 
    * @param newCommand
-   *                new command value
+   *          new command value
    * @param isError
-   *                true to set error color ends with #??
+   *          true to set error color ends with #??
    * 
    * @throws BadLocationException
    */