patched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)

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

diff --git a/src/jalview/gui/ScriptWindow.java b/src/jalview/gui/ScriptWindow.java
index ff377f7..652830d 100644 (file)
--- a/src/jalview/gui/ScriptWindow.java
+++ b/src/jalview/gui/ScriptWindow.java
@@ -29,6 +29,7 @@ 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
 {
@@ -53,7 +54,7 @@ public final class ScriptWindow extends JPanel implements ActionListener,
 
   public ScriptWindow(AppJmol appJmol)
   {
-    this.viewer = appJmol.viewer;
+    this.viewer = appJmol.jmb.viewer;
     this.appJmol = appJmol;
 
     setLayout(new BorderLayout());
@@ -230,7 +231,7 @@ 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");