X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=66f180be4c72186c75934d0e2cb817a4dd865b8f;hb=c6f74fc7b3c9bcf8571435e5f52169d72581af15;hp=cfc9f9472139dde27c2e9e215d87208813234b17;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index cfc9f94..66f180b 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -18,8 +18,6 @@
  */
 package jalview.schemes;
 
-import java.util.*;
-
 import java.awt.*;
 
 import jalview.datamodel.*;
@@ -39,31 +37,34 @@ public class PIDColourScheme
 
   public Color findColour(String s, int j)
   {
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z')
+    {
+      s = String.valueOf(res -= ('a' - 'A'));
+    }
+
+
     if ( (threshold != 0) && !aboveThreshold(s, j))
     {
       return Color.white;
     }
 
-    Color c = Color.white;
-    Hashtable hash = (Hashtable) consensus.elementAt(j);
+    currentColour = Color.white;
 
     double sc = 0;
 
-    if ( (Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
-        hash.contains(s))
+    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
+        consensus[j].contains(s))
     {
-      sc = ( ( (Integer) hash.get(s)).intValue() * 100.0) /
-          ( (Integer) hash.get(
-              "size")).intValue();
+      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
 
-      // MC Should be isGap
-      if (!jalview.util.Comparison.isGap( (s.charAt(0))))
+      if (!jalview.util.Comparison.isGap( res ))
       {
         for (int i = 0; i < thresholds.length; i++)
         {
           if (sc > thresholds[i])
           {
-            c = pidColours[i];
+            currentColour = pidColours[i];
 
             break;
           }
@@ -71,6 +72,9 @@ public class PIDColourScheme
       }
     }
 
-    return c;
+    if(conservationColouring)
+         applyConservation(j);
+
+    return currentColour;
   }
 }