[Biojava-dev] Error trying to write a sequence in memory to system.out in FASTA format

[David Huen]

On Tue, 12 Aug 2003, Carlisia P. Campos wrote:

> Hello there,
> 
> I am trying to write a sequence in memory to system.out in FASTA format 
> and I get the exception below. If anyone has a work around pls let me 
> know.
> 
> Thank you,
> --Carlisia
> 
>      try{
>        Sequence seq = DNATools.createDNASequence("atggct", "seq");
>        SeqIOTools.writeFasta(System.out, seq);        <--- breaking here
>      }
>      catch (IOException ioe)
>      {
>        ioe.printStackTrace();
>      }
>      catch (IllegalSymbolException ex) {
>        //this will happen if you try and make the DNA seq using non IUB 
> symbols
>        ex.printStackTrace();
>      }
> 
> 
> Exception in thread "main" java.lang.NoClassDefFoundError: 
> org/apache/regexp/RESyntaxException
> 	at 
> com.carlisia.ws.bio.TranscribeDNAtoRNA.main(TranscribeDNAtoRNA.java:74)
> Process exited with exit code 1.
> 

It seems to be telling you that you do not have the regexp jar in your
system/classpath.  You are presumably on Java-1.3? You will need to get
and install it.

Rgds,
dh