Formatting changes

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

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 9c720ee..1aea477 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,63 +1,78 @@
 /*\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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
 package jalview.schemes;\r
 \r
-import java.awt.*;\r
-\r
 import java.util.*;\r
 \r
+import java.awt.*;\r
 \r
-public class Blosum62ColourScheme extends ResidueColourScheme {\r
-    public Blosum62ColourScheme() {\r
-        super();\r
+public class Blosum62ColourScheme\r
+    extends ResidueColourScheme\r
+{\r
+  public Blosum62ColourScheme()\r
+  {\r
+    super();\r
+  }\r
+\r
+  public Color findColour(String s, int j)\r
+  {\r
+    if ( (threshold != 0) && !aboveThreshold(s, j))\r
+    {\r
+      return Color.white;\r
     }\r
 \r
-    public Color findColour(String s, int j) {\r
-        if ((threshold != 0) && !aboveThreshold(s, j)) {\r
-            return Color.white;\r
+    Hashtable hash = (Hashtable) consensus.elementAt(j);\r
+\r
+    if (!jalview.util.Comparison.isGap( (s.charAt(0))))\r
+    {\r
+      String max = (String) hash.get("maxResidue");\r
+\r
+      if (max.indexOf(s) > -1)\r
+      {\r
+        return 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
+        do\r
+        {\r
+          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
+              max_aa + 1), s);\r
         }\r
+        while (++max_aa < n);\r
 \r
-        Hashtable hash = (Hashtable) consensus.elementAt(j);\r
-\r
-        if (!jalview.util.Comparison.isGap((s.charAt(0)))) {\r
-            String max = (String) hash.get("maxResidue");\r
-\r
-            if (max.indexOf(s) > -1) {\r
-                return new Color(154, 154, 255);\r
-            } else {\r
-                int c = 0;\r
-                int max_aa = 0;\r
-                int n = max.length();\r
-\r
-                do {\r
-                    c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
-                            max_aa + 1), s);\r
-                } while (++max_aa < n);\r
-\r
-                if (c > 0) {\r
-                    return new Color(204, 204, 255);\r
-                } else {\r
-                    return Color.white;\r
-                }\r
-            }\r
-        } else {\r
-            return Color.white;\r
+        if (c > 0)\r
+        {\r
+          return new Color(204, 204, 255);\r
         }\r
+        else\r
+        {\r
+          return Color.white;\r
+        }\r
+      }\r
+    }\r
+    else\r
+    {\r
+      return Color.white;\r
     }\r
+  }\r
 }\r