X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=a79f0833da6dc4ffcc7d25e1b9b315cf6a10bc56;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=3d1c18b7f5c726482b8e22efd71b6fde3fa9690d;hpb=83b55697263efc7b0c660eba6ea7091f6904257d;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 3d1c18b..a79f083 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -49,31 +49,35 @@ public class PIDColourScheme
       return Color.white;
     }
 
-
-
-    Color c = Color.white;
+    currentColour = Color.white;
 
     double sc = 0;
 
-    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
-        consensus[j].contains(s))
-    {
-      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
+    if(consensus.length<=j)
+      return Color.white;
 
-      if (!jalview.util.Comparison.isGap( res ))
+      if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
+          consensus[j].contains(s))
       {
-        for (int i = 0; i < thresholds.length; i++)
+        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
+
+        if (!jalview.util.Comparison.isGap(res))
         {
-          if (sc > thresholds[i])
+          for (int i = 0; i < thresholds.length; i++)
           {
-            c = pidColours[i];
+            if (sc > thresholds[i])
+            {
+              currentColour = pidColours[i];
 
-            break;
+              break;
+            }
           }
         }
       }
-    }
 
-    return c;
+    if(conservationColouring)
+         applyConservation(j);
+
+    return currentColour;
   }
 }