JAL-2599 complete documentation for HMM and HMMFile classes

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 57e00fe..8ff95a1 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -728,15 +728,15 @@ public class AAFrequency
   }
 
   /**
-   * produces a HMM profile for a column in an alignment
+   * Produces a HMM profile for a column in an alignment
    * 
    * @param aa
-   *          Alignment annotation for which the profile is being calculated
+   *          Alignment annotation for which the profile is being calculated.
    * @param column
-   *          column in the alignment the profile is being made for
+   *          Column in the alignment the profile is being made for.
    * @param removeBelowBackground
-   *          boolean, indicating whether to ignore residues with probabilities
-   *          less than their background frequencies
+   *          Boolean indicating whether to ignore residues with probabilities
+   *          less than their background frequencies.
    * @return
    */
   public static int[] getHMMProfileFor(AlignmentAnnotation aa, int column,