[Biojava-l] BioException Error

[Brian Cox]

I am getting a BioException Error thrown on a new MAC but the same code and
BioJava version running on a windows box and a older MAC are okay. Is there
any known issue with newer MACs?
 
the error is:
AlignExtractTF.java:221: cannot access BioException
bad class file: ./BioException.java
file does not contain class BioException
Please remove or make sure it appears in the correct subdirectory of
the classpath.
        public void mapSequence(File fileName)throws
FileNotFoundException, IOException{
                                                                       
    ^
1 error
 
 
the problematic code is;
 
 
 public void mapSequence(File fileName)throws FileNotFoundException,
IOException{
  try{
   BufferedReader in = new BufferedReader (new FileReader (fileName));
   SequenceIterator si =
(SequenceIterator)SeqIOTools.fileToBiojava("fasta","dna", in);
   while (si.hasNext()){
    Sequence seq = si.nextSequence();
    seqMap.put(seq.getName(), seq.seqString());
    seqAvailible.append(seq.getName()+"\n");
   } 
 
  }
  catch (FileNotFoundException ex) {
  //can't find file specified 
  ex.printStackTrace();
  }
  catch (BioException ex) {
  //error parsing requested format
  ex.printStackTrace();
  }

 
thanks
 
 
Brian Cox
Samuel Lunenfeld Research Institute
Mount Sinai Hospital, Rm 884
Toronto, Ontario
Canada
 
416-586-8266