X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=00f8f6f6bb1c597eb1af80cf05d222367bc12052;hb=c1e70ea0a01d2c916675aa8020970c6696d0dba5;hp=41fc6c9d66fb3cad17bced928d4986143cd5cd3c;hpb=b5d69834ef8b11df514d5b4c08c82945f15f8a2e;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 41fc6c9..00f8f6f 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -147,12 +147,11 @@ public class UserColourScheme
         {
           token = st2.nextToken();
 
-          int colIndex =
-              ( (Integer) ResidueProperties.aaHash.
-               get(token)).intValue();
+          if (ResidueProperties.aaIndex[token.charAt(0)]==-1)
+            continue;
+
+          int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
 
-           //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
-           /*
           if(token.equalsIgnoreCase("lowerCase"))
           {
             if (lowerCaseColours == null)
@@ -172,7 +171,7 @@ public class UserColourScheme
             }
             lowerCaseColours[colIndex] = getColourFromString(colour);
           }
-          else*/
+          else
             colors[colIndex] = getColourFromString(colour);
         }
       }
@@ -187,16 +186,16 @@ public class UserColourScheme
 
 
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
-      int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
+      Color currentColour;
+      int index = ResidueProperties.aaIndex[c];
 
-      if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+      if ((threshold == 0) || aboveThreshold(c, j))
       {
-       //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
-       /* if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
+        if(lowerCaseColours!=null && 'a' <= c && c <= 'z')
           currentColour = lowerCaseColours[index];
-        else*/
+        else
           currentColour = colors[index];
       }
       else
@@ -205,7 +204,7 @@ public class UserColourScheme
       }
 
       if(conservationColouring)
-        applyConservation(j);
+       currentColour =  applyConservation(currentColour, j);
 
 
       return currentColour;