X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;fp=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=77cbd9235eaf133ef3049437953a6507d18ad774;hb=469dc5a0e6d06a2c8a27f27b712ccfdbe3314ee4;hp=0486744cadcfecbd2e8b4a01f91c7d3670f580e9;hpb=f32142e854e6eadb5c85c4379d596369bd7098c5;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 0486744..77cbd92 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -229,12 +229,13 @@ public class CommandLineOperations
     String ln = null;
     while ((ln = worker.getOutputReader().readLine()) != null)
     {
-      System.out.println(ln);
+      System.out.println("STDOUT: " + ln);
       successfulCMDs.add(ln);
     }
     while ((ln = worker.getErrorReader().readLine()) != null)
     {
-      System.err.println(ln);
+      System.err.println("STDERR: " + ln);
+      successfulCMDs.add(ln);
     }
   }
 
@@ -247,6 +248,7 @@ public class CommandLineOperations
 
     // number of lines expected on STDERR when Jalview starts up normally
     // may need to adjust this if Jalview is excessively noisy ?
+    final int STDOUT_SETUPLINES = 50;
     final int STDERR_SETUPLINES = 50;
 
     // thread monitors stderr - bails after SETUP_TIMEOUT or when
@@ -257,14 +259,24 @@ public class CommandLineOperations
       public void run()
       {
         String ln = null;
-        int count = 0;
+        int stdoutcount = 0;
+        int stderrcount = 0;
         try
         {
           while ((ln = worker.getOutputReader().readLine()) != null)
           {
             System.out.println(ln);
             successfulCMDs.add(ln);
-            if (++count > STDERR_SETUPLINES)
+            if (++stdoutcount > STDOUT_SETUPLINES)
+            {
+              break;
+            }
+          }
+          while ((ln = worker.getErrorReader().readLine()) != null)
+          {
+            System.err.println(ln);
+            successfulCMDs.add(ln);
+            if (++stderrcount > STDERR_SETUPLINES)
             {
               break;
             }