Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3cae900..d437f1b 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -107,7 +107,7 @@ public class Jalview
         perms.add(new AllPermission());
         return (perms);
       }
-
+    
       @Override
       public void refresh()
       {
@@ -124,8 +124,8 @@ public class Jalview
   class FeatureFetcher
   {
     /*
-     * TODO: generalise to track all jalview events to orchestrate batch processing
-     * events.
+     * TODO: generalise to track all jalview events to orchestrate batch
+     * processing events.
      */
 
     private int queued = 0;
@@ -343,8 +343,7 @@ public class Jalview
     }
 
     /*
-     * configure 'full' SO model if preferences say to, else use the default (SO
-     * Lite)
+     * configure 'full' SO model 
      */
     if (Cache.getDefault("USE_FULL_SO", true))
     {
@@ -421,7 +420,6 @@ public class Jalview
       BioJsHTMLOutput.updateBioJS();
     }
 
-    Cache.log.info("CHECKPOINT 1");
     // Move any new getdown-launcher-new.jar into place over old
     // getdown-launcher.jar
     String appdirString = System.getProperty("getdownappdir");
@@ -446,7 +444,6 @@ public class Jalview
     DataSourceType protocol = null;
     FileLoader fileLoader = new FileLoader(!headless);
 
-    Cache.log.info("CHECKPOINT 2");
     String groovyscript = null; // script to execute after all loading is
     // completed one way or another
     // extract groovy argument and execute if necessary