X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=8dd8994d8f61f93d7045b9513c27568bc381ce96;hb=cb25f36c03700f3d42099d89a4f676c5d6cc63d7;hp=4c20873c4a62a690dda22d31636ece89670ca1a4;hpb=d640a8ce605b836b2e6eb1771994d3baef5c31a0;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 4c20873..8dd8994 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -70,23 +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 =  ResidueProperties.aaIndex[seq.charAt(i)];
+          res = ResidueProperties.aaIndex[seq[i]];
         }
 
         cons2[i][res]++;
@@ -240,22 +240,21 @@ 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)
   {
     Color currentColour;
 
-
-    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(s, j)))
+    if (cons2.length <= j || (threshold != 0 && !aboveThreshold(c, j)))
     {
       return Color.white;
     }
 
-    int i = ResidueProperties.aaIndex[s.charAt(0)];
+    int i = ResidueProperties.aaIndex[c];
 
     currentColour = Color.white;
 
@@ -264,13 +263,13 @@ public class ClustalxColourScheme
       return currentColour;
     }
 
-  for (int k = 0; k < ResidueColour[i].conses.length; k++)
-  {
-    if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
+    for (int k = 0; k < ResidueColour[i].conses.length; k++)
     {
-      currentColour = ResidueColour[i].c;
+      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
+      {
+        currentColour = ResidueColour[i].c;
+      }
     }
-  }
 
     if (i == 4)
     {
@@ -280,8 +279,10 @@ public class ClustalxColourScheme
       }
     }
 
-    if(conservationColouring)
+    if (conservationColouring)
+    {
       currentColour = applyConservation(currentColour, j);
+    }
 
     return currentColour;
   }