X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=86868948cbaabc6905181855e9ce8f6ac46c030c;hb=f78ed026becc8e143d5b5953fce6c0961428d2a7;hp=1575a6a5d8a7a1f87f1138cca08995bc8c48cf31;hpb=1774759f889464551c244c070b7771dabbb4bad2;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 1575a6a..8686894 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
@@ -35,33 +36,38 @@ public class PIDColourScheme
     this.thresholds = ResidueProperties.pidThresholds;
   }
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
-    char res = s.charAt(0);
-    if ('a' <= res && res <= 'z')
+    if ('a' <= c && c <= 'z')
     {
-      s = String.valueOf(res -= ('a' - 'A'));
+      c -= ('a' - 'A');
     }
 
+    if (consensus == null
+        || j >= consensus.length
+        || consensus[j]==null)
+    {
+      return Color.white;
+    }
 
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    if ( (threshold != 0) && !aboveThreshold(c, j))
     {
       return Color.white;
     }
 
-    currentColour = Color.white;
+    Color currentColour = Color.white;
 
     double sc = 0;
 
     if(consensus.length<=j)
       return Color.white;
 
-      if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
-          consensus[j].contains(s))
+      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
+          consensus[j].contains(String.valueOf(c)))
       {
         sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
 
-        if (!jalview.util.Comparison.isGap(res))
+        if (!jalview.util.Comparison.isGap(c))
         {
           for (int i = 0; i < thresholds.length; i++)
           {
@@ -76,7 +82,7 @@ public class PIDColourScheme
       }
 
     if(conservationColouring)
-         applyConservation(j);
+      currentColour = applyConservation(currentColour, j);
 
     return currentColour;
   }