Format changes

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index addf00f..4c20873 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 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
@@ -86,8 +86,7 @@ public class ClustalxColourScheme
         }\r
         else\r
         {\r
-          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +\r
-              "")).intValue();\r
+          res =  ResidueProperties.aaIndex[seq.charAt(i)];\r
         }\r
 \r
         cons2[i][res]++;\r
@@ -248,37 +247,43 @@ public class ClustalxColourScheme
 \r
   public Color findColour(String s, int j)\r
   {\r
-    if ( (threshold != 0) && !aboveThreshold(s, j))\r
+    Color currentColour;\r
+\r
+\r
+    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(s, j)))\r
     {\r
       return Color.white;\r
     }\r
 \r
-    int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();\r
+    int i = ResidueProperties.aaIndex[s.charAt(0)];\r
 \r
-    Color c = Color.white;\r
+    currentColour = Color.white;\r
 \r
     if (i > 19)\r
     {\r
-      return c;\r
+      return currentColour;\r
     }\r
 \r
-    for (int k = 0; k < ResidueColour[i].conses.length; k++)\r
+  for (int k = 0; k < ResidueColour[i].conses.length; k++)\r
+  {\r
+    if (ResidueColour[i].conses[k].isConserved(cons2, j, size))\r
     {\r
-      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))\r
-      {\r
-        c = ResidueColour[i].c;\r
-      }\r
+      currentColour = ResidueColour[i].c;\r
     }\r
+  }\r
 \r
     if (i == 4)\r
     {\r
       if (conses[27].isConserved(cons2, j, size))\r
       {\r
-        c = (Color) colhash.get("PINK");\r
+        currentColour = (Color) colhash.get("PINK");\r
       }\r
     }\r
 \r
-    return c;\r
+    if(conservationColouring)\r
+      currentColour = applyConservation(currentColour, j);\r
+\r
+    return currentColour;\r
   }\r
 }\r
 \r