X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=0db55c03c8b0946692a5709acc6fa28744358476;hb=bcb00c5d25c6c0783a5057ab23a267d81cc1e353;hp=40243f27e76abff749da6e981c6a6ea05f85d285;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 40243f2..0db55c0 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,68 +1,94 @@
 /*
-* 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.schemes;
 
-
-import java.util.*;
 import java.awt.*;
 
-public class Blosum62ColourScheme extends ResidueColourScheme
-{
+import jalview.analysis.*;
 
+public class Blosum62ColourScheme
+    extends ResidueColourScheme
+{
   public Blosum62ColourScheme()
   {
     super();
   }
 
-  public Color findColour(String s, int j)
+  public Color findColour(char res, int j)
   {
-    if( threshold!=0 && !aboveThreshold(s,j))
+    if ('a' <= res && res <= 'z')
+    {
+      // TO UPPERCASE !!!
+      res -= ('a' - 'A');
+    }
+
+    if (consensus == null ||
+        j >= consensus.length ||
+        consensus[j] == null ||
+        (threshold != 0 && !aboveThreshold(res, j)))
+    {
       return Color.white;
+    }
 
-    Hashtable hash = (Hashtable)consensus.elementAt(j);
+    Color currentColour;
 
-    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(AAFrequency.MAXRESIDUE);
 
-      if (max.indexOf(s)>-1)
-        return new Color(154, 154, 255);
-      else {
+      if (max.indexOf(res) > -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.charAt(max_aa), res);
+        }
+        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)
+      {
+        currentColour = applyConservation(currentColour, j);
       }
     }
     else
-        return Color.white;
+    {
+      return Color.white;
+    }
 
+    return currentColour;
   }
-
-
 }