JAL-3130 incorporating feature/JAL-3063jaxbNoCastor and new script utils/jdeps_jlink_...

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index f213abe..fc922b9 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -47,10 +47,9 @@ public class PIDColourScheme extends ResidueColourScheme
           String consensusResidue, float pid)
   {
     /*
-     * make everything uppercase; note this does nothing
-     * if consensusResidue is already uppercase
+     * compare as upper case; note consensusResidue is 
+     * always computed as uppercase
      */
-    consensusResidue = consensusResidue.toUpperCase();
     if ('a' <= c && c <= 'z')
     {
       c -= ('a' - 'A');
@@ -66,8 +65,7 @@ public class PIDColourScheme extends ResidueColourScheme
     /*
      * test whether this is the consensus (or joint consensus) residue
      */
-    boolean matchesConsensus = consensusResidue.contains(
-            String.valueOf(c));
+    boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
     if (matchesConsensus)
     {
       for (int i = 0; i < thresholds.length; i++)