X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=c11e1ecee6b18adcc25a1f55878a8262f8cde1b6;hb=6ddf2d553aee329db44dd36b564211c3880563ec;hp=b69e536cfa30384bf30b07eb992fdea38795d9f0;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index b69e536..c11e1ec 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -52,6 +52,26 @@ public class ScoreColourScheme extends ResidueColourScheme
         this.scores = scores;
         this.min = min;
         this.max = max;
+
+        // Make colours in constructor
+        // Why wasn't this done earlier?
+        int i, iSize=scores.length;
+        colors = new Color[scores.length];
+        for (i = 0; i < iSize; i++)
+        {
+          float red = (float) (scores[i] - (float) min) / (float) (max - min);
+
+          if (red > 1.0f)
+          {
+            red = 1.0f;
+          }
+
+          if (red < 0.0f)
+          {
+            red = 0.0f;
+          }
+          colors[i] = makeColour(red);
+        }
     }
 
     /**
@@ -72,19 +92,6 @@ public class ScoreColourScheme extends ResidueColourScheme
             }
         }
 
-        float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -
-            (float) min) / (float) (max - min);
-
-        if (red > 1.0f)
-        {
-            red = 1.0f;
-        }
-
-        if (red < 0.0f)
-        {
-            red = 0.0f;
-        }
-
         char c = s.charAt(0);
 
         if (jalview.util.Comparison.isGap((c)))
@@ -92,8 +99,12 @@ public class ScoreColourScheme extends ResidueColourScheme
             return Color.white;
         }
 
-        // This isn';t great - pool of colours in here?
-        return makeColour(red);
+        currentColour = colors[((Integer) ResidueProperties.aaHash.get(s)).intValue()];
+
+        if(conservationColouring)
+         applyConservation(j);
+
+        return currentColour;
     }
 
     /**