X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=df905006fe4f1fe03ac5112a1b15e13799258a84;hb=f78ed026becc8e143d5b5953fce6c0961428d2a7;hp=b905c452ba87dcce2683ded2f74c2ec0fdc5cd36;hpb=d640a8ce605b836b2e6eb1771994d3baef5c31a0;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b905c45..df90500 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -75,21 +75,20 @@ public class ResidueColourScheme implements ColourSchemeI
     /**
     * Find a colour without an index in a sequence
     */
-   public Color findColour(String aa)
+   public Color findColour(char c)
    {
-       return colors[ResidueProperties.aaIndex[aa.charAt(0)]];
+       return colors[ResidueProperties.aaIndex[c]];
    }
 
 
 
-   public Color findColour(String s, int j)
+   public Color findColour(char c, int j)
    {
        Color currentColour;
-       int index = ResidueProperties.aaIndex[s.charAt(0)];
 
-       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+       if ((threshold == 0) || aboveThreshold(c, j))
        {
-           currentColour = colors[index];
+           currentColour = colors[ResidueProperties.aaIndex[c]];
        }
        else
        {
@@ -136,22 +135,20 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @return DOCUMENT ME!
      */
-    public boolean aboveThreshold(String s, int j)
+    public boolean aboveThreshold(char c, int j)
     {
-      char c = s.charAt(0);
       if ('a' <= c && c <= 'z')
         {
           // TO UPPERCASE !!!
           //Faster than toUpperCase
           c -= ('a' - 'A');
-          s = String.valueOf(c);
         }
 
         if (consensus == null || consensus[j] == null)
           return false;
 
         if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
-            consensus[j].contains(s))
+            consensus[j].contains(String.valueOf(c)))
         {
           if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
           {