JAL-98 javadoc / comments updated

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 5ecd644..569b036 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -111,7 +111,9 @@ public class AAFrequency
    * 
    * @param sequences
    * @param start
+   *          start column (inclusive, base zero)
    * @param end
+   *          end column (exclusive)
    * @param result
    *          array in which to store profile per column
    * @param saveFullProfile
@@ -169,8 +171,7 @@ public class AAFrequency
         else
         {
           /*
-           * here we count a gap if the sequence doesn't
-           * reach this column (is that correct?)
+           * count a gap if the sequence doesn't reach this column
            */
           residueCounts.addGap();
         }
@@ -220,8 +221,8 @@ public class AAFrequency
   /**
    * Derive the consensus annotations to be added to the alignment for display.
    * This does not recompute the raw data, but may be called on a change in
-   * display options, such as 'show logo', which may in turn result in a change
-   * in the derived values.
+   * display options, such as 'ignore gaps', which may in turn result in a
+   * change in the derived values.
    * 
    * @param consensus
    *          the annotation row to add annotations to