imported properties via -props should never be overwritten

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 75fb618..f77c2f1 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -227,6 +227,9 @@ public class Cache
     {
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
+    } else {
+      // don't corrupt the file we've been given.
+      propsAreReadOnly = true;
     }
 
     try