X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=e1dbf4696706b9cd4b8c96bb4a6cf7f76d8a04cf;hb=1a0f6886ffdb431de180af2089db4910a1dfb564;hp=66f180be4c72186c75934d0e2cb817a4dd865b8f;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 66f180b..e1dbf46 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) 2007 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
@@ -20,6 +20,7 @@ package jalview.schemes;
 
 import java.awt.*;
 
+import jalview.analysis.*;
 import jalview.datamodel.*;
 
 public class PIDColourScheme
@@ -35,30 +36,41 @@ 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 ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
-        consensus[j].contains(s))
+    if (consensus.length <= j)
     {
-      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
+      return Color.white;
+    }
 
-      if (!jalview.util.Comparison.isGap( res ))
+    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(c))
       {
         for (int i = 0; i < thresholds.length; i++)
         {
@@ -72,8 +84,10 @@ public class PIDColourScheme
       }
     }
 
-    if(conservationColouring)
-         applyConservation(j);
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
 
     return currentColour;
   }