CurrentColour must not be accessed by multiple sequence renderers

[jalview.git] / src / jalview / schemes / Blosum62ColourScheme.java

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 2e18c6a..d3b93bf 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,5 +1,6 @@
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998  Michele Clamp\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -13,20 +14,17 @@
  *\r
  * You should have received a copy of the GNU General Public License\r
  * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  */\r
-\r
 package jalview.schemes;\r
 \r
 \r
-import java.util.*;\r
 import java.awt.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
+import jalview.analysis.AAFrequency;\r
 \r
-public class Blosum62ColourScheme extends ResidueColourScheme\r
+public class Blosum62ColourScheme\r
+    extends ResidueColourScheme\r
 {\r
-\r
   public Blosum62ColourScheme()\r
   {\r
     super();\r
@@ -34,37 +32,63 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 \r
   public Color findColour(String s, int j)\r
   {\r
-    Hashtable hash = (Hashtable)consensus.elementAt(j);\r
 \r
-    if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
+    char res = s.charAt(0);\r
+    if ('a' <= res && res <= 'z' )\r
     {\r
-      String    max  = (String)hash.get("maxResidue");\r
+       // TO UPPERCASE !!!\r
+       s = String.valueOf( res -= ('a' - 'A') );\r
+    }\r
 \r
-      if (max.indexOf(s)>-1)\r
-        return new Color(154, 154, 255);\r
-      else {\r
+    if (consensus == null ||\r
+        j >= consensus.length ||\r
+        consensus[j] == null ||\r
+        (threshold != 0 && !aboveThreshold(s, j)))\r
+    {\r
+      return Color.white;\r
+    }\r
 \r
-        int c = 0,\r
-            max_aa=0,\r
-            n=max.length();\r
-        do {\r
-          c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);\r
-        } while (++max_aa<n);\r
+    Color currentColour;\r
+\r
+    if (!jalview.util.Comparison.isGap( res ))\r
+    {\r
+      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);\r
+\r
+      if (max.indexOf(s) > -1)\r
+      {\r
+        currentColour = new Color(154, 154, 255);\r
+      }\r
+      else\r
+      {\r
+        int c = 0;\r
+        int max_aa = 0;\r
+        int n = max.length();\r
 \r
-        if (c>0)\r
-          return new Color(204, 204, 255);\r
+        do\r
+        {\r
+          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
+              max_aa + 1), s);\r
+        }\r
+        while (++max_aa < n);\r
+\r
+        if (c > 0)\r
+        {\r
+          currentColour = new Color(204, 204, 255);\r
+        }\r
         else\r
-          return Color.white;\r
+        {\r
+          currentColour = Color.white;\r
+        }\r
       }\r
+\r
+      if(conservationColouring)\r
+         applyConservation(currentColour, j);\r
     }\r
     else\r
-        return Color.white;\r
-\r
-  }\r
+    {\r
+      return Color.white;\r
+    }\r
 \r
-  public boolean canThreshold()\r
-  {\r
-    return true;\r
+    return currentColour;\r
   }\r
-\r
 }\r