X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=155302137c2d8f1aad5243b75e86ba3375cf9f8d;hb=344e33b5217c85d7f237974224b0db367bcca667;hp=963bfbd9d492d27f1c8bd8f168b5b91bd71eeebc;hpb=05a51640d2a5c35cd32e8ad831963bd268ea10f6;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 963bfbd..1553021 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -193,16 +193,14 @@ public class AAFrequency
    *          The alignment column on which the first profile is based.
    * @param end
    *          The alignment column on which the last profile is based.
-   * @param saveFullProfile
-   *          if true, all residue counts are saved (enables profile logo)
    * @param removeBelowBackground
    *          if true, symbols with a match emission probability less than
    *          background frequency are ignored
    * @return
    */
   public static ProfilesI calculateHMMProfiles(final HiddenMarkovModel hmm,
-          int width, int start, int end, boolean saveFullProfile,
-          boolean removeBelowBackground, boolean infoLetterHeight)
+          int width, int start, int end, boolean removeBelowBackground,
+          boolean infoLetterHeight)
   {
     ProfileI[] result = new ProfileI[width];
     char[] symbols = hmm.getSymbols().toCharArray();
@@ -221,11 +219,7 @@ public class AAFrequency
       int gapCount = counts.getGapCount();
       ProfileI profile = new Profile(symbolCount, gapCount, maxCount,
               maxResidue);
-
-      if (saveFullProfile)
-      {
-        profile.setCounts(counts);
-      }
+      profile.setCounts(counts);
 
       result[column] = profile;
     }
@@ -380,16 +374,6 @@ public class AAFrequency
         // hmm consensus sequence is shorter than the alignment
         break;
       }
-      ProfileI profile = profiles.get(column);
-      if (profile == null)
-      {
-        /*
-         * happens if sequences calculated over were 
-         * shorter than alignment width
-         */
-        information.annotations[column] = null;
-        return 0f;
-      }
       
       float value = hmm.getInformationContent(column);
       boolean isNaN = Float.isNaN(value);