From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 9 Feb 2017 09:01:13 +0000 (+0000)
Subject: JAL-2371 skip upper-casing consensus as it already is
X-Git-Tag: Release_2_10_3b1~351
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eeb9907df14f1015db254a87bcc8db35e10ba02d;p=jalview.git

JAL-2371 skip upper-casing consensus as it already is
---

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 53670e3..f35b886 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -54,10 +54,9 @@ public class Blosum62ColourScheme extends ResidueColourScheme
           String consensusResidue, float pid)
   {
     /*
-     * compare as upper case; note toUpperCase does nothing 
-     * if the string is already uppercase
+     * compare as upper case; note consensusResidue is 
+     * always computed as uppercase
      */
-    consensusResidue = consensusResidue.toUpperCase();
     if ('a' <= res && res <= 'z')
     {
       res -= ('a' - 'A');
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index f213abe..657d6b0 100755
--- 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');