JAL-3010 fix up bad merge from develop

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0b1cf60..c41f291 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -70,9 +70,15 @@ import groovy.util.GroovyScriptEngine;
 /**
  * Main class for Jalview Application <br>
  * <br>
- * start with java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$"
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
  * jalview.bin.Jalview
  * 
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ * 
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -150,7 +156,6 @@ public class Jalview
           af.setProgressBar(MessageManager
                   .getString("status.das_features_being_retrived"), id);
           af.featureSettings_actionPerformed(null);
-          af.featureSettings.fetchDasFeatures(dasSources, true);
           af.setProgressBar(null, id);
           synchronized (us)
           {
@@ -321,7 +326,7 @@ public class Jalview
      * configure 'full' SO model if preferences say to, 
      * else use the default (SO Lite)
      */
-    if (Cache.getDefault("USE_FULL_SO", false))
+    if (Cache.getDefault("USE_FULL_SO", true))
     {
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }