[Biojava-l] Exception not being caught.

[Michael Heuer]

On Wed, 29 Dec 2004, Richard HOLLAND wrote:

> I am getting an exception thrown by my code that never seems to get
> caught. I am not sure if this is because of BioJava or because of a lack
> of understanding of Exceptions on my part? The exception causes the
> program to grind to an immediate halt. My method throws the general
> Exception class, but the exception thrown by BioJava seems to escape
> that detail and treats it as though my method were not handling
> exceptions at all. I would expect the calling method which wraps the
> call in a try{}catch{Exception e} statement to catch it? But apparently
> not? Why not?!!
>
> The method in BioJava I am using is DNATools.createDNASequence.
>
> Here is the exception:
>
> Exception in thread "main" org.biojava.bio.BioError: Something has gone
> badly wrong with DNA
>         at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:158)

Unfortunately BioError is not an exception, it is an Error.

I believe you can catch them with

try
{
  // ...
}
catch (Throwable t)
{
  // ...
}

but you probably shouldn't be.  From the BioError javadoc:

For developers:
Throw this when something has gone wrong and in general people should
not be handling it.



> org.biojava.bio.seq.DNATools.createDNASequence(DNATools.java:176)
>         at
> gis.aads.pipeline.LibraryFastaBuilder.run(LibraryFastaBuilder.java:234)
>         at gis.pipeline.Main.main(Main.java:125)
> Caused by: org.biojava.bio.symbol.IllegalSymbolException: This
> tokenization doesn't contain character: ''
>         at
> org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTok
> enization.java:175)

This is the real problem:  the parser doesn't know what to do with the
character ''.  I don't know exactly what that means, but does the string
you pull out of the database clob look reasonable?

   michael


> And here is the method that calls it (or bits of it anyhow, and an
> example calling method):
>
>     public void doTheThing() {
> 	 MyClass otherClass = new MyClass();
>        try {
>   	    int rc = otherClass.run();
> 	    System.out.println("rc was "+rc);
>        } catch (Exception e) {
>           System.out.println("oops!");
>        }
>     }
>
>     public int run() throws Exception {
> ....
>         // For each library, get all trimmed seqs.
>         for (String lib : libs) {
>             log.info("Processing library "+lib);
> ....
>             // Get the sequences.
>             seqq.execute(lib);
>             rs = seqq.results();
>
>             // Log info.
>             log.info("Processing fasta.");
>             while (rs.next()) {
>                 // Get details.
>                 String seqID = rs.getString(1);
>                 char direction = UserSampleID.getDirection(seqID);
>                 Clob seqclob = rs.getClob(2);
>                 String seqstr =
> seqclob.getSubString((long)1,(int)seqclob.length());
>                 if (seqstr.length()<minLength) continue;
>
>                 // Create the sequence and format it into fasta.
>                 Sequence seq = DNATools.createDNASequence(seqstr,
> seqID);
>                 ByteArrayOutputStream baos = new
> ByteArrayOutputStream();
>                 SeqIOTools.writeFasta(baos,seq);
>                 baos.flush();
>
>                 // For each seq, if reverse, add to reverse temp file.
>                 // Else, add to forward temp file.
>                 switch (direction) {
>                     case 'R':
>                         reverseWriter.write(baos.toString());
>                         break;
>                     case 'F':
>                         forwardWriter.write(baos.toString());
>                         break;
>                     default:
>                         log.warning("Unknown direction "+direction+"
> received for sequence "+seqID);
>                         rc = PipelineApp.FAILURE;
>                         continue;
>                 }
> ....
>             }
> ....
>         }
> ....
>     }
>
>
> I understand that the exception is thrown because of an invalid
> sequence, but I don't understand why it isn't being caught.
>
>
> Richard Holland
> Bioinformatics Specialist
> GIS extension 8199
>
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