From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 27 Apr 2017 10:57:50 +0000 (+0100)
Subject: JAL-1933 shade occupancy from light grey to black for high -> low occupancy
X-Git-Tag: Release_2_10_2~3^2~124^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0af11fd54aa58f2b17e5f940391cb880e61bc57f;p=jalview.git

JAL-1933 shade occupancy from light grey to black for high -> low occupancy
---

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index ddf1bbb..3636b5e 100755
--- 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);
@@ -333,8 +335,8 @@ public class AAFrequency
       String description = "";
 
       gaprow.annotations[i] = new Annotation(description, description,
-              '\0',
-              gapped);
+              '\0', gapped, jalview.util.ColorUtils.bleachColour(
+                      Color.DARK_GRAY, (float) scale * gapped));
     }
   }