X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=e1b60cafac5e8d50419c31bc6503c5b127f4e383;hb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;hp=aa20121dc616bf9489ff9d5937ad8ca7050f62d7;hpb=c430867beda6dcf8236f59d1346ff4b026b0b62b;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index aa20121..e1b60ca 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -23,6 +23,7 @@ package jalview.schemes;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.Map;
@@ -35,13 +36,10 @@ import java.util.Map;
  */
 public class ScoreColourScheme extends ResidueColourScheme
 {
-  /** DOCUMENT ME!! */
   public double min;
 
-  /** DOCUMENT ME!! */
   public double max;
 
-  /** DOCUMENT ME!! */
   public double[] scores;
 
   /**
@@ -65,25 +63,38 @@ public class ScoreColourScheme extends ResidueColourScheme
 
     // Make colours in constructor
     // Why wasn't this done earlier?
-    int i, iSize = scores.length;
+    int iSize = scores.length;
     colors = new Color[scores.length];
-    for (i = 0; i < iSize; i++)
+    for (int i = 0; i < iSize; i++)
     {
-      float red = (float) (scores[i] - (float) min) / (float) (max - min);
+      /*
+       * scale score between min and max to the range 0.0 - 1.0
+       */
+      float score = (float) (scores[i] - (float) min) / (float) (max - min);
 
-      if (red > 1.0f)
+      if (score > 1.0f)
       {
-        red = 1.0f;
+        score = 1.0f;
       }
 
-      if (red < 0.0f)
+      if (score < 0.0f)
       {
-        red = 0.0f;
+        score = 0.0f;
       }
-      colors[i] = makeColour(red);
+      colors[i] = makeColour(score);
     }
   }
 
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    if (Comparison.isGap(c))
+    {
+      return Color.white;
+    }
+    return super.findColour(c);
+  }
+
   /**
    * DOCUMENT ME!
    *