X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=df905006fe4f1fe03ac5112a1b15e13799258a84;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=bf8366547f6d93fb38e857de28994fd5c3b3b758;hpb=3d941a02a998676a12f8ff43fa98d9e1f4c27142;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index bf83665..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
        {
@@ -97,7 +96,7 @@ public class ResidueColourScheme implements ColourSchemeI
        }
 
        if(conservationColouring)
-         applyConservation(currentColour, j);
+         currentColour = applyConservation(currentColour, j);
 
 
        return currentColour;
@@ -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)
           {
@@ -221,7 +218,7 @@ public class ResidueColourScheme implements ColourSchemeI
     * @return DOCUMENT ME!
     */
 
-   void applyConservation(Color currentColour, int i)
+   Color applyConservation(Color currentColour, int i)
    {
 
      if ((conservation[i] != '*') && (conservation[i] != '+'))
@@ -235,8 +232,7 @@ public class ResidueColourScheme implements ColourSchemeI
          float t = 11 - (conservation[i] - '0');
          if(t==0)
          {
-           currentColour = Color.white;
-           return;
+           return Color.white;
          }
 
          int red = currentColour.getRed();
@@ -261,6 +257,7 @@ public class ResidueColourScheme implements ColourSchemeI
            currentColour = new Color(red, green, blue);
        }
        }
+       return currentColour;
    }