Proceed with upperCase residue

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 356e3fe..4b1bf15 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -31,13 +31,19 @@ public class Blosum62ColourScheme
 \r
   public Color findColour(String s, int j)\r
   {\r
+    char res = s.charAt(0);\r
+    if ('a' <= res && res <= 'z' )\r
+    {\r
+       s = Character.toString( res -= ('a' - 'A') );\r
+    }\r
+\r
+\r
     if ( (threshold != 0) && !aboveThreshold(s, j))\r
     {\r
       return Color.white;\r
     }\r
 \r
-\r
-    if (!jalview.util.Comparison.isGap( (s.charAt(0))))\r
+    if (!jalview.util.Comparison.isGap( res ))\r
     {\r
       String max = (String) consensus[j].get("maxResidue");\r
 \r

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 8cea507..9dc4c66 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -37,11 +37,20 @@ public class PIDColourScheme
 \r
   public Color findColour(String s, int j)\r
   {\r
+    char res = s.charAt(0);\r
+    if ('a' <= res && res <= 'z')\r
+    {\r
+      s = Character.toString(res -= ('a' - 'A'));\r
+    }\r
+\r
+\r
     if ( (threshold != 0) && !aboveThreshold(s, j))\r
     {\r
       return Color.white;\r
     }\r
 \r
+\r
+\r
     Color c = Color.white;\r
 \r
     double sc = 0;\r
@@ -51,7 +60,7 @@ public class PIDColourScheme
     {\r
       sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
 \r
-      if (!jalview.util.Comparison.isGap( (s.charAt(0))))\r
+      if (!jalview.util.Comparison.isGap( res ))\r
       {\r
         for (int i = 0; i < thresholds.length; i++)\r
         {\r