X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=2c0836de99c6d7dec867547d7579e9c3cd4c30e2;hb=91c5d2144a780716e755e99882acffe46b40f18f;hp=566d7edcb7efa621cdbafdb0ee4664e91de0b640;hpb=66b1bf1a6480b320ddaa00d4f5e70b2051041c11;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 566d7ed..2c0836d 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,5 +1,6 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
@@ -13,18 +14,16 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemes;
 
 
-import java.util.*;
 import java.awt.*;
 
-public class Blosum62ColourScheme extends ResidueColourScheme
+public class Blosum62ColourScheme
+    extends ResidueColourScheme
 {
-
   public Blosum62ColourScheme()
   {
     super();
@@ -32,36 +31,58 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
   public Color findColour(String s, int j)
   {
-    if( threshold!=0 && !aboveThreshold(s,j))
-      return Color.white;
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z' )
+    {
+       // TO UPPERCASE !!!
+       s = String.valueOf( res -= ('a' - 'A') );
+    }
+
 
-    Hashtable hash = (Hashtable)consensus.elementAt(j);
+    if ( j>=consensus.length || (threshold != 0 && !aboveThreshold(s, j) ))
+    {
+      return Color.white;
+    }
 
-    if (!jalview.util.Comparison.isGap((s.charAt(0))))
+    if (!jalview.util.Comparison.isGap( res ))
     {
-      String    max  = (String)hash.get("maxResidue");
+      String max = (String) consensus[j].get("maxResidue");
 
-      if (max.indexOf(s)>-1)
-        return new Color(154, 154, 255);
-      else {
+      if (max.indexOf(s) > -1)
+      {
+        currentColour = new Color(154, 154, 255);
+      }
+      else
+      {
+        int c = 0;
+        int max_aa = 0;
+        int n = max.length();
 
-        int c = 0,
-            max_aa=0,
-            n=max.length();
-        do {
-          c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);
-        } while (++max_aa<n);
+        do
+        {
+          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
+              max_aa + 1), s);
+        }
+        while (++max_aa < n);
 
-        if (c>0)
-          return new Color(204, 204, 255);
+        if (c > 0)
+        {
+          currentColour = new Color(204, 204, 255);
+        }
         else
-          return Color.white;
+        {
+          currentColour = Color.white;
+        }
       }
+
+      if(conservationColouring)
+         applyConservation(j);
     }
     else
-        return Color.white;
+    {
+      return Color.white;
+    }
 
+    return currentColour;
   }
-
-
 }