JAL-1933 gap value as description; minor formatting

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index e682e2c..0e055e4 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,6 +20,10 @@
  */
 package jalview.analysis;
 
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -37,10 +41,6 @@ import jalview.util.Format;
 import jalview.util.MappingUtils;
 import jalview.util.QuickSort;
 
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-
 /**
  * Takes in a vector or array of sequences and column start and column end and
  * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
@@ -67,8 +67,8 @@ public class AAFrequency
     }
   }
 
-  public static final ProfilesI calculate(List<SequenceI> list,
-          int start, int end)
+  public static final ProfilesI calculate(List<SequenceI> list, int start,
+          int end)
   {
     return calculate(list, start, end, false);
   }
@@ -303,7 +303,6 @@ public class AAFrequency
   public static void completeGapAnnot(AlignmentAnnotation consensus,
           ProfilesI profiles, int startCol, int endCol, long nseq)
   {
-    // long now = System.currentTimeMillis();
     if (consensus == null || consensus.annotations == null
             || consensus.annotations.length < endCol)
     {
@@ -331,12 +330,11 @@ public class AAFrequency
 
       final int gapped = profile.getGapped();
 
-      String description = "" + gapped;
+      String description = String.valueOf(gapped);
 
-      consensus.annotations[i] = new Annotation(gapped);
+      consensus.annotations[i] = new Annotation("", description, '0',
+              gapped);
     }
-    // long elapsed = System.currentTimeMillis() - now;
-    // System.out.println(-elapsed);
   }
 
   /**
@@ -408,8 +406,7 @@ public class AAFrequency
    *          calculations
    * @return
    */
-  public static int[] extractProfile(ProfileI profile,
-          boolean ignoreGaps)
+  public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
   {
     int[] rtnval = new int[64];
     ResidueCount counts = profile.getCounts();