X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=ee16f9455665b7c698c84664941896ad2d1e8473;hb=8537d486848be3e97578248dae6bede12e343fe1;hp=e682e2ca2091f5e82a41f70737953503c042cbba;hpb=41c34ccf7054239554932deca6f64042231977b5;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index e682e2c..ee16f94 100755
--- 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);
   }
@@ -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
@@ -300,12 +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)
   {
-    // long now = System.currentTimeMillis();
-    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 
@@ -314,8 +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);
@@ -325,18 +324,18 @@ 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 = "" + gapped;
+      String description = String.valueOf(gapped);
 
-      consensus.annotations[i] = new Annotation(gapped);
+      gaprow.annotations[i] = new Annotation(description, description,
+              '\0',
+              gapped);
     }
-    // long elapsed = System.currentTimeMillis() - now;
-    // System.out.println(-elapsed);
   }
 
   /**
@@ -408,8 +407,7 @@ 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();