JAL-3949 read ~/.jalview_properties before initialising the logging

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 920c86d..f01cbb6 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -284,17 +284,6 @@ public class Jalview
       System.out.println("Launcher version: " + val);
     }
 
-    try
-    {
-      Cache.initLogger();
-    } catch (NoClassDefFoundError error)
-    {
-      error.printStackTrace();
-      System.out.println("\nEssential logging libraries not found."
-              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
-      System.exit(0);
-    }
-
     // report Jalview version
     Cache.loadBuildProperties(true);
 
@@ -377,6 +366,17 @@ public class Jalview
     System.setProperty("http.agent",
             "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
 
+    try
+    {
+      Cache.initLogger();
+    } catch (NoClassDefFoundError error)
+    {
+      error.printStackTrace();
+      System.out.println("\nEssential logging libraries not found."
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
+      System.exit(0);
+    }
+
     desktop = null;
 
     setLookAndFeel();