Formatted source

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 34c47ed..2535154 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,52 +16,52 @@
 * 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
 import jalview.datamodel.*;\r
-import java.util.*;\r
+\r
 import java.awt.*;\r
 \r
+import java.util.*;\r
+\r
+\r
 public class PIDColourScheme extends ResidueColourScheme {\r
     public Color[] pidColours;\r
     public float[] thresholds;\r
-\r
     SequenceGroup group;\r
 \r
     public PIDColourScheme() {\r
-       this.pidColours = ResidueProperties.pidColours;\r
-       this.thresholds = ResidueProperties.pidThresholds;\r
+        this.pidColours = ResidueProperties.pidColours;\r
+        this.thresholds = ResidueProperties.pidThresholds;\r
     }\r
 \r
+    public Color findColour(String s, int j) {\r
+        if ((threshold != 0) && !aboveThreshold(s, j)) {\r
+            return Color.white;\r
+        }\r
 \r
+        Color c = Color.white;\r
+        Hashtable hash = (Hashtable) consensus.elementAt(j);\r
 \r
-  public Color findColour(String s, int j) {\r
+        double sc = 0;\r
 \r
-    if( threshold!=0 && !aboveThreshold(s,j))\r
-      return Color.white;\r
+        if ((Integer.parseInt(hash.get("maxCount").toString()) != -1) &&\r
+                hash.contains(s)) {\r
+            sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(\r
+                    "size")).intValue();\r
 \r
-    Color     c    = Color.white;\r
-      Hashtable hash =  (Hashtable)consensus.elementAt(j);\r
+            // MC Should be isGap\r
+            if (!jalview.util.Comparison.isGap((s.charAt(0)))) {\r
+                for (int i = 0; i < thresholds.length; i++) {\r
+                    if (sc > thresholds[i]) {\r
+                        c = pidColours[i];\r
 \r
-      double sc = 0;\r
-      if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
-      {\r
-        sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;\r
-        // MC Should be isGap\r
-        if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
-        {\r
-          for (int i = 0; i < thresholds.length; i++)\r
-          {\r
-            if (sc > thresholds[i])\r
-            {\r
-              c = pidColours[i];\r
-              break;\r
+                        break;\r
+                    }\r
+                }\r
             }\r
-          }\r
         }\r
 \r
-      }\r
-      return c;\r
-  }\r
+        return c;\r
+    }\r
 }\r