X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=ee16f9455665b7c698c84664941896ad2d1e8473;hb=8537d486848be3e97578248dae6bede12e343fe1;hp=0e055e450a3ae6983946062d4e28bf56c39ab551;hpb=679e63aab1a22d128bf429a07514eb15f8b288e1;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 0e055e4..ee16f94 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -291,7 +291,7 @@ public class AAFrequency
   /**
    * Derive the gap count annotation row.
    * 
-   * @param consensus
+   * @param gaprow
    *          the annotation row to add annotations to
    * @param profiles
    *          the source consensus data
@@ -300,11 +300,11 @@ public class AAFrequency
    * @param endCol
    *          end column (exclusive)
    */
-  public static void completeGapAnnot(AlignmentAnnotation consensus,
+  public static void completeGapAnnot(AlignmentAnnotation gaprow,
           ProfilesI profiles, int startCol, int endCol, long nseq)
   {
-    if (consensus == null || consensus.annotations == null
-            || consensus.annotations.length < endCol)
+    if (gaprow == null || gaprow.annotations == null
+            || gaprow.annotations.length < endCol)
     {
       /*
        * called with a bad alignment annotation row 
@@ -313,8 +313,8 @@ public class AAFrequency
       return;
     }
     // always set ranges again
-    consensus.graphMax = nseq;
-    consensus.graphMin = 0;
+    gaprow.graphMax = nseq;
+    gaprow.graphMin = 0;
     for (int i = startCol; i < endCol; i++)
     {
       ProfileI profile = profiles.get(i);
@@ -324,15 +324,16 @@ public class AAFrequency
          * happens if sequences calculated over were 
          * shorter than alignment width
          */
-        consensus.annotations[i] = null;
+        gaprow.annotations[i] = null;
         return;
       }
 
-      final int gapped = profile.getGapped();
+      final int gapped = profile.getNonGapped();
 
       String description = String.valueOf(gapped);
 
-      consensus.annotations[i] = new Annotation("", description, '0',
+      gaprow.annotations[i] = new Annotation(description, description,
+              '\0',
               gapped);
     }
   }