X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=0691d82d47e10dd93bb8721fb3866f8ce860a917;hb=c3c305755d392741176209a0274a47897ac4d8a8;hp=df9d535aa1045354d18cdae3746fe15666f9a949;hpb=9832a6ac361db1a51c020ef1ebdb7f495676c72d;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index df9d535..0691d82 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -114,8 +114,7 @@ public abstract class AlignFile extends FileParse
     protected boolean isValidProteinSequence(String sequence)
     {
         for (int i = 0; i < sequence.length(); i++)
-            if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
-                        String.valueOf(sequence.charAt(i))))
+            if (jalview.schemes.ResidueProperties.aaIndex[sequence.charAt(i)]==-1)
             {
                 invalidCharacter = sequence.charAt(i);
                 return false;