This constructor is never called

[jalview.git] / src / jalview / schemes / UserColourScheme.java

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index bd70c5d..00f8f6f 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -147,14 +147,10 @@ public class UserColourScheme
         {\r
           token = st2.nextToken();\r
 \r
-          if (ResidueProperties.aaHash.get(token) == null)\r
+          if (ResidueProperties.aaIndex[token.charAt(0)]==-1)\r
             continue;\r
 \r
-          int colIndex =\r
-              ( (Integer) ResidueProperties.aaHash.\r
-               get(token)).intValue();\r
-\r
-           //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+          int colIndex = ResidueProperties.aaIndex[token.charAt(0)];\r
 \r
           if(token.equalsIgnoreCase("lowerCase"))\r
           {\r
@@ -190,14 +186,14 @@ public class UserColourScheme
 \r
 \r
 \r
-  public Color findColour(String s, int j)\r
+  public Color findColour(char c, int j)\r
   {\r
-      int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();\r
+      Color currentColour;\r
+      int index = ResidueProperties.aaIndex[c];\r
 \r
-      if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
+      if ((threshold == 0) || aboveThreshold(c, j))\r
       {\r
-       //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
-        if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')\r
+        if(lowerCaseColours!=null && 'a' <= c && c <= 'z')\r
           currentColour = lowerCaseColours[index];\r
         else\r
           currentColour = colors[index];\r
@@ -208,7 +204,7 @@ public class UserColourScheme
       }\r
 \r
       if(conservationColouring)\r
-        applyConservation(j);\r
+       currentColour =  applyConservation(currentColour, j);\r
 \r
 \r
       return currentColour;\r