From 7be3a744db5213f49e70178ade126d1cc797c762 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 6 Oct 2006 13:50:44 +0000
Subject: [PATCH] Set consensus as hashtble[]

---
 src/jalview/schemes/ColourSchemeI.java       |    2 +-
 src/jalview/schemes/ResidueColourScheme.java |   22 +++++++++++++++-------
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 124a24a..da3093e 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -26,7 +26,7 @@ public interface ColourSchemeI
 
   public Color findColour(String s, int j);
 
-  public void setConsensus(java.util.Vector v);
+  public void setConsensus(java.util.Hashtable [] h);
 
   public void setConservation(jalview.analysis.Conservation c);
 
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 0d2db23..a993802 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -144,7 +144,17 @@ public class ResidueColourScheme implements ColourSchemeI
      */
     public boolean aboveThreshold(String s, int j)
     {
-        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
+      char c = s.charAt(0);
+      if ('a' <= c && c <= 'z')
+        {
+          // TO UPPERCASE !!!
+          //Faster than toUpperCase
+          c -= ('a' - 'A');
+          s = String.valueOf(c);
+        }
+
+
+      if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
                 consensus[j].contains(s))
         {
             if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)
@@ -177,18 +187,16 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @param consensus DOCUMENT ME!
      */
-    public void setConsensus(Vector vconsensus)
+    public void setConsensus(Hashtable [] consensus)
     {
-      if(vconsensus==null)
+      if(consensus==null)
         return;
 
-       int i, iSize=vconsensus.size();
-       consensus = new Hashtable[iSize];
-       for(i=0; i<iSize; i++)
-        consensus[i] = (Hashtable)vconsensus.elementAt(i);
+      this.consensus = consensus;
     }
 
 
+
     public void setConservation(Conservation cons)
     {
       if(cons==null)
-- 
1.7.10.2