X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=ec5d4f1517aa4f3e120097d4a268f8ddc7761c92;hb=ecb5ab32cb7599f6665117ad4e25c61f0a650720;hp=d91d49fe0410f19ec7349259d745c6229e404936;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d91d49f..ec5d4f1 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) 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
@@ -13,51 +14,78 @@
  *
  * 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.*;
-import jalview.gui.*;
-import jalview.datamodel.*;
+import jalview.analysis.AAFrequency;
 
-public class Blosum62ColourScheme extends ResidueColourScheme
+public class Blosum62ColourScheme
+    extends ResidueColourScheme
 {
-
-  // need to keep an eye on the changing visible consensus sequence
-  AlignViewport av;
-
-  public Blosum62ColourScheme(AlignViewport av)
+  public Blosum62ColourScheme()
   {
     super();
-    this.av = av;
   }
 
-  public Color findColour(SequenceI seq, String s, int j, Vector aa)
+  public Color findColour(String s, int j)
   {
-      if (!s.equals("-") && !s.equals(".") && !s.equals(" "))
-      {
-        String max = av.getVisibleConsensus().charAt(j) + "";
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z' )
+    {
+       // TO UPPERCASE !!!
+       s = String.valueOf( res -= ('a' - 'A') );
+    }
 
-        if (s.equals(max))
-          return new Color(154, 154, 255);
-        else if (ResidueProperties.getBLOSUM62(max, s) > 0)
-          return new Color(204, 204, 255);
-        else
-          return Color.white;
+    if (consensus == null ||
+        j >= consensus.length ||
+        consensus[j] == null ||
+        (threshold != 0 && !aboveThreshold(s, j)))
+    {
+      return Color.white;
+    }
+
+    if (!jalview.util.Comparison.isGap( res ))
+    {
+      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
 
+      if (max.indexOf(s) > -1)
+      {
+        currentColour = new Color(154, 154, 255);
       }
       else
-        return Color.white;
+      {
+        int c = 0;
+        int max_aa = 0;
+        int n = max.length();
 
-  }
+        do
+        {
+          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
+              max_aa + 1), s);
+        }
+        while (++max_aa < n);
 
-  public boolean canThreshold()
-  {
-    return false;
-  }
+        if (c > 0)
+        {
+          currentColour = new Color(204, 204, 255);
+        }
+        else
+        {
+          currentColour = Color.white;
+        }
+      }
+
+      if(conservationColouring)
+         applyConservation(j);
+    }
+    else
+    {
+      return Color.white;
+    }
 
+    return currentColour;
+  }
 }