X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=8cea5071aa04572c3a7fb34f1d1a56137cc03c08;hb=96786b7b949dc261a9556e13a17870166915d0e9;hp=cfc9f9472139dde27c2e9e215d87208813234b17;hpb=0997f09413464c310de0fe1ad5a24d232b0bd2cf;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index cfc9f94..8cea507 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.*;
@@ -45,18 +43,14 @@ public class PIDColourScheme
     }
 
     Color c = Color.white;
-    Hashtable hash = (Hashtable) consensus.elementAt(j);
 
     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))))
       {
         for (int i = 0; i < thresholds.length; i++)