X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FScoreMatrixFile.java;h=ee7503d4012ccfe1a054087a80e29d16e92a639c;hb=bc7283e7d80b1f7f5fb7d95c51b96bb3af31593d;hp=0b70dce523589290b5bd64b09e0f902966161eb5;hpb=f6123f656fa387e11f506dedd09672a0d0ff5ac5;p=jalview.git

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>