From 44d74820a0af7a277c10c1eab98b59eb7fceddf6 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 4 Nov 2016 16:08:53 +0000
Subject: [PATCH] JAL-2292 squashed bug that breaks feature mapping for
 different cased residues

---
 src/MCview/PDBChain.java |    5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 7774dac..34f09c8 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -31,6 +31,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.List;
@@ -146,7 +147,9 @@ public class PDBChain
         pdbpos++;
       }
 
-      if (as.astr1.charAt(i) == as.astr2.charAt(i))
+      boolean sameResidue = Comparison.compareChars(as.astr1.charAt(i),
+              as.astr2.charAt(i), false);
+      if (sameResidue)
       {
         if (pdbpos >= residues.size())
         {
-- 
1.7.10.2