Report invalid chars

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index e72e0df..2ea1d2f 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -48,7 +48,7 @@ public class ClustalFile
     super.initData();\r
   }\r
 \r
-  public void parse()\r
+  public void parse() throws IOException\r
   {\r
     int i = 0;\r
     boolean flag = false;\r
@@ -131,6 +131,14 @@ public class ClustalFile
           Sequence newSeq = parseId(headers.elementAt(i).toString());\r
           newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );\r
 \r
+          if (!isValidProteinSequence(newSeq.getSequence()))\r
+          {\r
+              throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
+                                    + " : " + newSeq.getName()\r
+                                    + " : " + invalidCharacter);\r
+          }\r
+\r
+\r
           seqs.addElement(newSeq);\r
         }\r
         else\r