X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=ec5d4f1517aa4f3e120097d4a268f8ddc7761c92;hb=bc39ee8df9694f820a8a8bd2430f527b87c07f31;hp=9c720ee99d67cc6902dce73b0f857c719a277d01;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 9c720ee..ec5d4f1 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,63 +1,91 @@
 /*
-* 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) 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
+ * 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.awt.*;
+import jalview.analysis.AAFrequency;
 
-import java.util.*;
+public class Blosum62ColourScheme
+    extends ResidueColourScheme
+{
+  public Blosum62ColourScheme()
+  {
+    super();
+  }
 
+  public Color findColour(String s, int j)
+  {
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z' )
+    {
+       // TO UPPERCASE !!!
+       s = String.valueOf( res -= ('a' - 'A') );
+    }
 
-public class Blosum62ColourScheme extends ResidueColourScheme {
-    public Blosum62ColourScheme() {
-        super();
+    if (consensus == null ||
+        j >= consensus.length ||
+        consensus[j] == null ||
+        (threshold != 0 && !aboveThreshold(s, j)))
+    {
+      return Color.white;
     }
 
-    public Color findColour(String s, int j) {
-        if ((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
+      {
+        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);
 
-        Hashtable hash = (Hashtable) consensus.elementAt(j);
-
-        if (!jalview.util.Comparison.isGap((s.charAt(0)))) {
-            String max = (String) hash.get("maxResidue");
-
-            if (max.indexOf(s) > -1) {
-                return new Color(154, 154, 255);
-            } else {
-                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);
-
-                if (c > 0) {
-                    return new Color(204, 204, 255);
-                } else {
-                    return Color.white;
-                }
-            }
-        } else {
-            return Color.white;
+        if (c > 0)
+        {
+          currentColour = new Color(204, 204, 255);
         }
+        else
+        {
+          currentColour = Color.white;
+        }
+      }
+
+      if(conservationColouring)
+         applyConservation(j);
     }
+    else
+    {
+      return Color.white;
+    }
+
+    return currentColour;
+  }
 }