- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqstrings[i].toString(),\r
- Integer.parseInt(starts.elementAt(i).toString()),\r
- Integer.parseInt(ends.elementAt(i).toString()));\r
+ Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
+ seqstrings[i].toString(),\r
+ Integer.parseInt(starts.elementAt(i).\r
+ toString()),\r
+ Integer.parseInt(ends.elementAt(i).toString()));\r
+\r
+ if (!isValidProteinSequence(newSeq.getSequence()))\r
+ {\r
+ throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
+ +" : "+ newSeq.getName()\r
+ +" : "+invalidCharacter);\r
+\r
+ }\r
+\r