JAL-629 javadoc

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 86ebca9..efd2177 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1829,10 +1829,23 @@ public class Jalview
    * 
    * TEST OUTPUT METHODS
    * 
+   * these operate only when Arg.TESTOUTPUT has been passed, and variously check
+   * if an expected value / arg was set and report it to the test framework.
+   * 
    ******************************/
   /**
-   * method for reporting string values parsed/processed during tests
+   * report string values parsed/processed during tests When the Bootstrap
+   * argument Arg.TESTOUTPUT is present - reports on debug if given s1 is not
+   * null and not equals s2, warns if given argument is not set, and calls
+   * testoutput(true,a,s1,s2) to report processing progress.
    * 
+   * @param ap
+   *          - ArgParser handling parsing
+   * @param a
+   *          - Arg currently being processed
+   * @param s1
+   *          - expected 
+   * @param s2
    */
   protected static void testoutput(ArgParser ap, Arg a, String s1,
           String s2)
@@ -1857,7 +1870,9 @@ public class Jalview
   }
 
   /**
-   * method for reporting string values parsed/processed during tests
+   * report values passed via bootstrap arguments
+   * 
+   * TODO: significant code duplication with testouput(Argparser...) - move it
    */
 
   protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
@@ -1885,7 +1900,7 @@ public class Jalview
   }
 
   /**
-   * report value set for string values parsed/processed during tests
+   * conditionally (on @param yes) report that expected value s1 was set during CommandsTest tests
    */
   private static void testoutput(boolean yes, Arg a, String s1, String s2)
   {