finalize all these hashtables

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

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d91d49f..6e91e0b 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) 2005 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
@@ -13,51 +14,75 @@
  *\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
 \r
-public class Blosum62ColourScheme extends ResidueColourScheme\r
+public class Blosum62ColourScheme\r
+    extends ResidueColourScheme\r
 {\r
-\r
-  // need to keep an eye on the changing visible consensus sequence\r
-  AlignViewport av;\r
-\r
-  public Blosum62ColourScheme(AlignViewport av)\r
+  public Blosum62ColourScheme()\r
   {\r
     super();\r
-    this.av = av;\r
   }\r
 \r
-  public Color findColour(SequenceI seq, String s, int j, Vector aa)\r
+  public Color findColour(String s, int j)\r
   {\r
-      if (!s.equals("-") && !s.equals(".") && !s.equals(" "))\r
-      {\r
-        String max = av.getVisibleConsensus().charAt(j) + "";\r
+    char res = s.charAt(0);\r
+    if ('a' <= res && res <= 'z' )\r
+    {\r
+       // TO UPPERCASE !!!\r
+       s = String.valueOf( res -= ('a' - 'A') );\r
+    }\r
 \r
-        if (s.equals(max))\r
-          return new Color(154, 154, 255);\r
-        else if (ResidueProperties.getBLOSUM62(max, s) > 0)\r
-          return new Color(204, 204, 255);\r
-        else\r
-          return Color.white;\r
 \r
+    if ( (threshold != 0) && !aboveThreshold(s, j))\r
+    {\r
+      return Color.white;\r
+    }\r
+\r
+    if (!jalview.util.Comparison.isGap( res ))\r
+    {\r
+      String max = (String) consensus[j].get("maxResidue");\r
+\r
+      if (max.indexOf(s) > -1)\r
+      {\r
+        currentColour = new Color(154, 154, 255);\r
       }\r
       else\r
-        return Color.white;\r
+      {\r
+        int c = 0;\r
+        int max_aa = 0;\r
+        int n = max.length();\r
 \r
-  }\r
+        do\r
+        {\r
+          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
+              max_aa + 1), s);\r
+        }\r
+        while (++max_aa < n);\r
 \r
-  public boolean canThreshold()\r
-  {\r
-    return false;\r
-  }\r
+        if (c > 0)\r
+        {\r
+          currentColour = new Color(204, 204, 255);\r
+        }\r
+        else\r
+        {\r
+          currentColour = Color.white;\r
+        }\r
+      }\r
 \r
+      if(conservationColouring)\r
+         applyConservation(j);\r
+    }\r
+    else\r
+    {\r
+      return Color.white;\r
+    }\r
+\r
+    return currentColour;\r
+  }\r
 }\r