X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=ace752973215601be7c9fd6c45a991af72a8394f;hb=60541afc96ff3a4f5b79b78009922f373cbc29c3;hp=9fbfb8341ddbc925339ed5016383e2b765b863eb;hpb=04e88679fd837e9fe36d186e5eacdd5f13a89927;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 9fbfb83..ace7529 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -378,6 +378,8 @@ public class Desktop extends GDesktop
    */
   public Desktop(boolean forInstance)
   {
+
+    Cache.initLogger();
     instanceOnly = true;
   }
   
@@ -388,6 +390,7 @@ public class Desktop extends GDesktop
   @SuppressWarnings("unused")
   private Desktop()
   {
+    Cache.initLogger();
     try
     {
     /**
@@ -906,7 +909,7 @@ public class Desktop extends GDesktop
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (Desktop.getInstance().instanceOnly || Jalview.isHeadlessMode())
+    if (Jalview.isHeadlessMode() || Desktop.getInstance().instanceOnly)
     {
       return;
     }