X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=225f8dd467280f7658a395c8a1d3a2486fb74619;hb=b78278b3ee2cb653c439fa207b78a469d53ce697;hp=89e94fde391669525c0cbfc00a5c471ec34b3476;hpb=df7fd106ef48a8c4cb515785d9d82e711b530aa0;p=jalview.git

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 89e94fd..225f8dd 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -22,35 +22,27 @@ public class ScoreColourScheme extends ResidueColourScheme {
     this.max = max;
   }
 
- /* public Color getColour(SequenceI seq, int j, Vector aa) {
-      Color c = Color.white;
-      String s = seq.getSequence(j,j+1);
+
+    public Color findColour(String s,int j,Vector aa)
+    {
 
       if (threshold > 0)
       {
-	  if (aboveThreshold(aa,seq,j,threshold))
-	      c = findColour(seq,s,j,aa);
+         if (!aboveThreshold(aa,s,j))
+             return Color.white;
       }
-      else if ( !s.equals("-")  && !s.equals(".") && !s.equals(" ") )
-	  c = findColour(seq,s,j,aa);
-     //  else
-	//  c = Color.white;
-
-      return c;
-  }*/
-
-    public Color findColour(SequenceI seq,String s,int j,Vector aa)
-    {
 
 	float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]
 			    - (float)min)/(float)(max - min);
-	if (red > (float)1.0)
-	    red = (float)1.0;
+	if (red > 1.0f)
+	    red = 1.0f;
+
+	if (red < 0.0f)
+	    red = 0.0f;
 
-	if (red < (float)0.0)
-	    red = (float)0.0;
+    char c = s.charAt(0);
 
-    if(s.equals(" ")|| s.equals(".")  || s.equals("-"))
+    if(jalview.util.Comparison.isGap((c)))
         return Color.white;
 
 	// This isn';t great - pool of colours in here?