documented privacy settings, fixed potential unhandled exception in groovy class...

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 1a22859..e89292a 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -81,7 +81,7 @@ import org.apache.log4j.*;
  * service</li>
  * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
  * service</li>
- * <li>USAGESTATS (true) Enable google analytics tracker for collecting usage
+ * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for collecting usage
  * statistics</li>
  * <li>DAS_LOCAL_SOURCE list of local das sources</li>
  * <li>SHOW_OVERVIEW boolean for overview window display</li>
@@ -102,6 +102,7 @@ import org.apache.log4j.*;
  * <li>DAS_ACTIVE_SOURCE list of active sources</li>
  * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
  * (false)</li>
+ * <li>VERSION_CHECK (true) check for the latest release version from www.jalview.org</li>
  * <li></li>
  * 
  * </ul>
@@ -244,6 +245,7 @@ public class Cache
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null
+            && getDefault("VERSION_CHECK",true)
             && (System.getProperty("java.awt.headless") == null || System
                     .getProperty("java.awt.headless").equals("false")))
     {
@@ -390,7 +392,18 @@ public class Cache
     }
     return obj;
   }
-
+  /**
+   * remove the specified property from the jalview properties file
+   * @param string
+   */
+  public static void removeProperty(String string)
+  {
+    applicationProperties.remove(string);
+    saveProperties();
+  }
+  /**
+   * save the properties to the jalview properties path
+   */
   public static void saveProperties()
   {
     try
@@ -473,6 +486,9 @@ public class Cache
           // Tell the user that debug is enabled
           lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
         }
+      } catch (Error e) {
+        groovyJarsArePresent = 0;
+        jalview.bin.Cache.log.debug("Groovy Classes are not present",e);
       } catch (Exception e)
       {
         groovyJarsArePresent = 0;