[Biojava-l] BioException Error

[Richard HOLLAND]

The machine you run your code on should make no difference at all in
this case. The problem is more likely to be with the Java environment on
your newer machine, and/or the way in which BioJava was compiled. It
does look like you may be running different versions of Java on the two
machines. This could be a major contributing factor, depending on the
vendors/versions of the two JREs you have installed.

However, from the exception trace it looks more like you might have some
of the individual BioJava .java files on your classpath, which
would/should not work (I'm surprised it does on your older machine if
the commands you use to run your program are the same on both!). Try
compiling the BioJava jar file on your newer machine (using the
build.xml Ant script supplied with the BioJava distribution), and adding
only the jar files it generates to your classpath. Make sure your
classpath contains nothing else (except other jar files your project
requires, that is).

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of Brian Cox
> Sent: Friday, May 20, 2005 6:44 AM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] BioException Error
> 
> 
> 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
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