Sequence is char []

[jalview.git] / src / jalview / schemes / Blosum62ColourScheme.java

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index f2d2c98..02545a3 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -30,20 +30,18 @@ public class Blosum62ColourScheme
     super();\r
   }\r
 \r
-  public Color findColour(String s, int j)\r
+  public Color findColour(char res, int j)\r
   {\r
-\r
-    char res = s.charAt(0);\r
     if ('a' <= res && res <= 'z' )\r
     {\r
        // TO UPPERCASE !!!\r
-       s = String.valueOf( res -= ('a' - 'A') );\r
+       res -= ('a' - 'A');\r
     }\r
 \r
     if (consensus == null ||\r
         j >= consensus.length ||\r
         consensus[j] == null ||\r
-        (threshold != 0 && !aboveThreshold(s, j)))\r
+        (threshold != 0 && !aboveThreshold(res, j)))\r
     {\r
       return Color.white;\r
     }\r
@@ -54,7 +52,7 @@ public class Blosum62ColourScheme
     {\r
       String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);\r
 \r
-      if (max.indexOf(s) > -1)\r
+      if (max.indexOf(res) > -1)\r
       {\r
         currentColour = new Color(154, 154, 255);\r
       }\r
@@ -66,8 +64,8 @@ public class Blosum62ColourScheme
 \r
         do\r
         {\r
-          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
-              max_aa + 1), s);\r
+          c += ResidueProperties.getBLOSUM62(\r
+              max.charAt(max_aa), res);\r
         }\r
         while (++max_aa < n);\r
 \r