JAL-629 Move more stdout messages to stderr when outputting file to stdout

[jalview.git] / src / jalview / bin / Console.java

diff --git a/src/jalview/bin/Console.java b/src/jalview/bin/Console.java
index 30fd530..7ac793d 100644 (file)
--- a/src/jalview/bin/Console.java
+++ b/src/jalview/bin/Console.java
@@ -43,7 +43,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outputMessage(message);
       t.printStackTrace();
     }
 
@@ -57,7 +57,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outputMessage(message);
     }
 
   }
@@ -70,7 +70,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outputMessage(message);
       t.printStackTrace();
     }
   }
@@ -83,7 +83,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outputMessage(message);
     }
 
   }
@@ -96,7 +96,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outputMessage(message);
       t.printStackTrace();
     }
 
@@ -110,7 +110,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outputMessage(message);
     }
 
   }
@@ -123,7 +123,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outputMessage(message);
     }
   }
 
@@ -135,7 +135,7 @@ public class Console
     }
     else
     {
-      System.out.println(message);
+      outputMessage(message);
       t.printStackTrace();
     }
 
@@ -306,6 +306,21 @@ public class Console
     }
   }
 
+  public static void outputMessage(String message)
+  {
+    // send message to stderr if output to stdout is expected
+    if (Jalview.getInstance() != null
+            && Jalview.getInstance().bootstrapArgs != null
+            && Jalview.getInstance().bootstrapArgs.outputToStdout())
+    {
+      System.err.println(message);
+    }
+    else
+    {
+      System.out.println(message);
+    }
+  }
+
   public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
 
 }