From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 12 Aug 2020 11:00:57 +0000 (+0100)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~16
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7c269dc87e6fda52db3d73d07bc5f3e879e1f681;hp=339d1bf247a3b0d000044892bee3d5668a8d9b11;p=jalview.git

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
---

diff --git a/src/jalview/io/ScoreMatrixFile.java b/src/jalview/io/ScoreMatrixFile.java
index 0b70dce..ee7503d 100644
--- a/src/jalview/io/ScoreMatrixFile.java
+++ b/src/jalview/io/ScoreMatrixFile.java
@@ -20,13 +20,13 @@
  */
 package jalview.io;
 
+import java.io.IOException;
+import java.util.StringTokenizer;
+
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.SequenceI;
 
-import java.io.IOException;
-import java.util.StringTokenizer;
-
 /**
  * A class that can parse a file containing a substitution matrix and register
  * it for use in Jalview
@@ -131,7 +131,8 @@ public class ScoreMatrixFile extends AlignFile
       {
         continue;
       }
-      if (data.toUpperCase().startsWith(SCOREMATRIX))
+      // equivalent to data.startsWithIgnoreCase(SCOREMATRIX)
+      if (data.regionMatches(true, 0, SCOREMATRIX, 0, SCOREMATRIX.length()))
       {
         /*
          * Parse name from ScoreMatrix <name>