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
_______________________________________________
Biojava-l mailing list - Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l
