X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=8dd8994d8f61f93d7045b9513c27568bc381ce96;hb=0eca27bca577e774acd5aefb165e7c6396a1995e;hp=1e38a6d00ec197ba359e48b0e8ce5899f5d3b2c4;hpb=1774759f889464551c244c070b7771dabbb4bad2;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 1e38a6d..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) 2005 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
@@ -70,24 +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 +240,21 @@ 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)
-      return 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;
 
@@ -267,13 +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)
     {
@@ -283,8 +279,10 @@ public class ClustalxColourScheme
       }
     }
 
-    if(conservationColouring)
-         applyConservation(j);
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
 
     return currentColour;
   }