Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index ee16f94..b806355 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,10 +20,6 @@
  */
 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;
@@ -41,6 +37,11 @@ import jalview.util.Format;
 import jalview.util.MappingUtils;
 import jalview.util.QuickSort;
 
+import java.awt.Color;
+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.
@@ -315,6 +316,7 @@ public class AAFrequency
     // always set ranges again
     gaprow.graphMax = nseq;
     gaprow.graphMin = 0;
+    double scale = 0.8/nseq;
     for (int i = startCol; i < endCol; i++)
     {
       ProfileI profile = profiles.get(i);
@@ -330,11 +332,11 @@ public class AAFrequency
 
       final int gapped = profile.getNonGapped();
 
-      String description = String.valueOf(gapped);
+      String description = "" + gapped;
 
-      gaprow.annotations[i] = new Annotation(description, description,
-              '\0',
-              gapped);
+      gaprow.annotations[i] = new Annotation("", description,
+              '\0', gapped, jalview.util.ColorUtils.bleachColour(
+                      Color.DARK_GRAY, (float) scale * gapped));
     }
   }