Any character non aa or nucleotide is a space

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index a800f06..3fa4ac2 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -121,20 +121,7 @@ public abstract class AlignFile extends FileParse
         }\r
     }\r
 \r
-    // Checks whether sequence is valid aa characters\r
-    protected boolean isValidProteinSequence(char [] sequence)\r
-    {\r
-        for (int i = 0; i < sequence.length; i++)\r
-            if (jalview.schemes.ResidueProperties.aaIndex[sequence[i]]==-1)\r
-            {\r
-                invalidCharacter = sequence[i];\r
-                return false;\r
-            }\r
-\r
-        return true;\r
-    }\r
 \r
-    char invalidCharacter;\r
 \r
     /**\r
      * This method must be implemented to parse the contents of the file.\r