Formatting

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

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index f2d2c98..0db55c0 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -18,9 +18,9 @@
  */\r
 package jalview.schemes;\r
 \r
-\r
 import java.awt.*;\r
-import jalview.analysis.AAFrequency;\r
+\r
+import jalview.analysis.*;\r
 \r
 public class Blosum62ColourScheme\r
     extends ResidueColourScheme\r
@@ -30,31 +30,29 @@ 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
+    if ('a' <= res && res <= 'z')\r
     {\r
-       // TO UPPERCASE !!!\r
-       s = String.valueOf( res -= ('a' - 'A') );\r
+      // TO UPPERCASE !!!\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
 \r
     Color currentColour;\r
 \r
-    if (!jalview.util.Comparison.isGap( res ))\r
+    if (!jalview.util.Comparison.isGap(res))\r
     {\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
@@ -81,8 +79,10 @@ public class Blosum62ColourScheme
         }\r
       }\r
 \r
-      if(conservationColouring)\r
-       currentColour =  applyConservation(currentColour, j);\r
+      if (conservationColouring)\r
+      {\r
+        currentColour = applyConservation(currentColour, j);\r
+      }\r
     }\r
     else\r
     {\r