X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;fp=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=4ffc022dc58e6337482405d3d604a617334bec6b;hb=6ef963034788a3499e25c1bbd8ccf850e18b3f94;hp=564e57d0112aebda9367834d101918211ccb71cf;hpb=8126d1deddd25b8bf138654bdebf153ad1693b19;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 564e57d..4ffc022 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -203,11 +203,21 @@ public class CommandLineOperations
     {
       System.out.println(ln);
       successfulCMDs.add(ln);
+      if (ln.equals(Jalview.TERMINATOR_LINE))
+      {
+        break;
+      }
     }
-    while ((ln = worker.getErrorReader().readLine()) != null)
+    if (worker != null && worker.exit == null)
     {
-      System.err.println(ln);
+      worker.interrupt();
+      Thread.currentThread().interrupt();
+      worker.process.destroy();
     }
+    // while ((ln = worker.getErrorReader().readLine()) != null)
+    // {
+    // System.err.println(ln);
+    // }
 
   }
 
@@ -224,6 +234,11 @@ public class CommandLineOperations
     {
       System.out.println(ln);
       successfulCMDs.add(ln);
+      if (ln.equals(Jalview.TERMINATOR_LINE))
+      {
+        break;
+      }
+
       if (++count > 5)
       {
         break;