X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=eaf2a5f96e10ce729406c13d848ff438439deac8;hb=8bb6d4ca134e9b72bfd44aff6a51c6b14185a69d;hp=1e38a6d00ec197ba359e48b0e8ce5899f5d3b2c4;hpb=1774759f889464551c244c070b7771dabbb4bad2;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 1e38a6d..eaf2a5f 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -70,24 +70,23 @@ public class ClustalxColourScheme
     int res;
     int i;
     int j = 0;
-    String seq;
+    char [] seq;
 
     while (j < seqs.size())
     {
       seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
 
-      int end_j = seq.length() - 1;
+      int end_j = seq.length - 1;
 
       for (i = start; i <= end_j; i++)
       {
-        if ( (seq.length() - 1) < i)
+        if ( (seq.length - 1) < i)
         {
           res = 23;
         }
         else
         {
-          res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +
-              "")).intValue();
+          res =  ResidueProperties.aaIndex[seq[i]];
         }
 
         cons2[i][res]++;
@@ -241,24 +240,22 @@ public class ClustalxColourScheme
     ResidueColour[19] = colours[0]; // V
   }
 
-  public Color findColour(String s)
+  public Color findColour(char c)
   {
     return Color.pink;
   }
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
-
-    if(cons2.length<=j)
-      return currentColour;
+    Color currentColour;
 
 
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(c, j)))
     {
       return Color.white;
     }
 
-    int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();
+    int i = ResidueProperties.aaIndex[c];
 
     currentColour = Color.white;
 
@@ -284,7 +281,7 @@ public class ClustalxColourScheme
     }
 
     if(conservationColouring)
-         applyConservation(j);
+      currentColour = applyConservation(currentColour, j);
 
     return currentColour;
   }