X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=7f4bebeae89016568d89bbe635c565f09fc6a1fe;hb=0bdaa0deb6ee514912d2ed730e19f618bc44cb69;hp=66f180be4c72186c75934d0e2cb817a4dd865b8f;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 66f180b..7f4bebe 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
@@ -21,6 +21,7 @@ package jalview.schemes;
 import java.awt.*;
 
 import jalview.datamodel.*;
+import jalview.analysis.AAFrequency;
 
 public class PIDColourScheme
     extends ResidueColourScheme
@@ -43,6 +44,11 @@ public class PIDColourScheme
       s = String.valueOf(res -= ('a' - 'A'));
     }
 
+    if (consensus == null ||
+        j >= consensus.length)
+    {
+      return Color.white;
+    }
 
     if ( (threshold != 0) && !aboveThreshold(s, j))
     {
@@ -53,24 +59,27 @@ public class PIDColourScheme
 
     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(AAFrequency.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++)
           {
-            currentColour = pidColours[i];
+            if (sc > thresholds[i])
+            {
+              currentColour = pidColours[i];
 
-            break;
+              break;
+            }
           }
         }
       }
-    }
 
     if(conservationColouring)
          applyConservation(j);