From 503ebba0021fa583fa7af58f9406f9234274fd7c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 18 Aug 2005 09:47:32 +0000
Subject: [PATCH] Proceed with upperCase residue

---
 src/jalview/schemes/Blosum62ColourScheme.java |   10 ++++++++--
 src/jalview/schemes/PIDColourScheme.java      |   11 ++++++++++-
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 356e3fe..4b1bf15 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -31,13 +31,19 @@ public class Blosum62ColourScheme
 
   public Color findColour(String s, int j)
   {
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z' )
+    {
+       s = Character.toString( res -= ('a' - 'A') );
+    }
+
+
     if ( (threshold != 0) && !aboveThreshold(s, j))
     {
       return Color.white;
     }
 
-
-    if (!jalview.util.Comparison.isGap( (s.charAt(0))))
+    if (!jalview.util.Comparison.isGap( res ))
     {
       String max = (String) consensus[j].get("maxResidue");
 
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 8cea507..9dc4c66 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -37,11 +37,20 @@ public class PIDColourScheme
 
   public Color findColour(String s, int j)
   {
+    char res = s.charAt(0);
+    if ('a' <= res && res <= 'z')
+    {
+      s = Character.toString(res -= ('a' - 'A'));
+    }
+
+
     if ( (threshold != 0) && !aboveThreshold(s, j))
     {
       return Color.white;
     }
 
+
+
     Color c = Color.white;
 
     double sc = 0;
@@ -51,7 +60,7 @@ public class PIDColourScheme
     {
       sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
 
-      if (!jalview.util.Comparison.isGap( (s.charAt(0))))
+      if (!jalview.util.Comparison.isGap( res ))
       {
         for (int i = 0; i < thresholds.length; i++)
         {
-- 
1.7.10.2