X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e4f9ec61be47c93a4bd46ba36c6cbd1c104ce732;hb=388622051f3d669942d9df63557c7a1401d7ff6d;hp=b29d9d72cc2d70e92729b7d3e6c0835fe7db6c32;hpb=b036a71275c547ea3875298480a9a61b36f80eae;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b29d9d7..e4f9ec6 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1005,9 +1005,7 @@ public class Jalview
             ex.printStackTrace(System.err);
           }
         }
-        // TODO - load PDB structure(s) to alignment JAL-629
-        // (associate with identical sequence in alignment, or a specified
-        // sequence)
+        
         if (groovyscript != null)
         {
           // Execute the groovy script after we've done all the rendering stuff
@@ -1800,8 +1798,14 @@ public class Jalview
     }
   }
 
-  /*
-   * testoutput for string values
+  /******************************
+   * 
+   * TEST OUTPUT METHODS
+   * 
+   ******************************/
+  /**
+   * method for reporting string values parsed/processed during tests
+   * 
    */
   protected static void testoutput(ArgParser ap, Arg a, String s1,
           String s2)
@@ -1825,6 +1829,10 @@ public class Jalview
     testoutput(true, a, s1, s2);
   }
 
+  /**
+   * method for reporting string values parsed/processed during tests
+   */
+
   protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
           String s2)
   {
@@ -1849,6 +1857,9 @@ public class Jalview
     testoutput(true, a, s1, s2);
   }
 
+  /**
+   * report value set for string values parsed/processed during tests
+   */
   private static void testoutput(boolean yes, Arg a, String s1, String s2)
   {
     if (yes && ((s1 == null && s2 == null)