Formatted source

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

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 40243f2..9c720ee 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -16,53 +16,48 @@
 * 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
-\r
 package jalview.schemes;\r
 \r
-\r
-import java.util.*;\r
 import java.awt.*;\r
 \r
-public class Blosum62ColourScheme extends ResidueColourScheme\r
-{\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
-      return Color.white;\r
-\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
-        return new Color(154, 154, 255);\r
-      else {\r
+import java.util.*;\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
 \r
-        if (c>0)\r
-          return new Color(204, 204, 255);\r
-        else\r
-          return Color.white;\r
-      }\r
+public class Blosum62ColourScheme extends ResidueColourScheme {\r
+    public Blosum62ColourScheme() {\r
+        super();\r
     }\r
-    else\r
-        return Color.white;\r
-\r
-  }\r
-\r
 \r
+    public Color findColour(String s, int j) {\r
+        if ((threshold != 0) && !aboveThreshold(s, j)) {\r
+            return Color.white;\r
+        }\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
+        }\r
+    }\r
 }\r