Set consensus as hashtble[]

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 124a24a..da3093e 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -26,7 +26,7 @@ public interface ColourSchemeI
 \r
   public Color findColour(String s, int j);\r
 \r
-  public void setConsensus(java.util.Vector v);\r
+  public void setConsensus(java.util.Hashtable [] h);\r
 \r
   public void setConservation(jalview.analysis.Conservation c);\r
 \r

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