Formatting

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 8686894..e1dbf46 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
@@ -20,8 +20,8 @@ package jalview.schemes;
 \r
 import java.awt.*;\r
 \r
+import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
-import jalview.analysis.AAFrequency;\r
 \r
 public class PIDColourScheme\r
     extends ResidueColourScheme\r
@@ -45,7 +45,7 @@ public class PIDColourScheme
 \r
     if (consensus == null\r
         || j >= consensus.length\r
-        || consensus[j]==null)\r
+        || consensus[j] == null)\r
     {\r
       return Color.white;\r
     }\r
@@ -59,30 +59,35 @@ public class PIDColourScheme
 \r
     double sc = 0;\r
 \r
-    if(consensus.length<=j)\r
+    if (consensus.length <= j)\r
+    {\r
       return Color.white;\r
+    }\r
 \r
-      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&\r
-          consensus[j].contains(String.valueOf(c)))\r
-      {\r
-        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
+    if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=\r
+          -1) &&\r
+        consensus[j].contains(String.valueOf(c)))\r
+    {\r
+      sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
 \r
-        if (!jalview.util.Comparison.isGap(c))\r
+      if (!jalview.util.Comparison.isGap(c))\r
+      {\r
+        for (int i = 0; i < thresholds.length; i++)\r
         {\r
-          for (int i = 0; i < thresholds.length; i++)\r
+          if (sc > thresholds[i])\r
           {\r
-            if (sc > thresholds[i])\r
-            {\r
-              currentColour = pidColours[i];\r
+            currentColour = pidColours[i];\r
 \r
-              break;\r
-            }\r
+            break;\r
           }\r
         }\r
       }\r
+    }\r
 \r
-    if(conservationColouring)\r
+    if (conservationColouring)\r
+    {\r
       currentColour = applyConservation(currentColour, j);\r
+    }\r
 \r
     return currentColour;\r
   }\r