X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=eae76e16821a3d75e273da6f69900f8152711283;hb=4265a395749b667cf7d558b8bad40ee2a57b6972;hp=6850d79f7c78f765417e87e7a9af99f0895d5bb3;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 6850d79..eae76e1 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -20,13 +20,12 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.awt.Color;
-import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -36,13 +35,10 @@ import java.util.Map;
  */
 public class ScoreColourScheme extends ResidueColourScheme
 {
-  /** DOCUMENT ME!! */
   public double min;
 
-  /** DOCUMENT ME!! */
   public double max;
 
-  /** DOCUMENT ME!! */
   public double[] scores;
 
   /**
@@ -66,35 +62,28 @@ 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);
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param j
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   @Override
   public Color findColour(char c, int j, SequenceI seq)
   {
@@ -102,8 +91,7 @@ public class ScoreColourScheme extends ResidueColourScheme
     {
       return Color.white;
     }
-
-    return colors[ResidueProperties.aaIndex[c]];
+    return super.findColour(c);
   }
 
   /**
@@ -130,8 +118,8 @@ public class ScoreColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
   {
     return new ScoreColourScheme(symbolIndex, scores, min, max);
   }