[Biojava-l] Pb running BIOJAVA

[Thomas Down]

The problem seems to be that you're trying to compile (very)
old code against a recent BioJava.  We changed the sequence
IO APIs signficantly between 1.0 and 1.1.  The change is
regrettable, but has made the APIs a lot more flexible.

Where did you get this version of TestEmbl.java?  If you
download a recent source release, you should get a working
version.  Alternatively, you can just replace the problematic
lines with something like:

    BufferedReader br = new BufferedReader(new FileReader(fileName));
    SequenceIterator seqI = SeqIOTools.readEmbl(br);

But it would be good to get the old versions out of circulation!

Let me know if you have any more trouble,

    Thomas.


On Thu, Sep 06, 2001 at 11:38:57AM +0900, TaeJin Ahn wrote:
> Dear biojava,
> 
> Thank for your nice work and sharing your product.
> I recently tried to run biojava product but failed with following message.
> I believe I configure classpath correctly.
> It seems all packages are called correctly but there is some still missing object.
> I hereby pasting error messages and jar file names I downloaded.
> 
> /*
> javac seq\TestEmbl.java
> seq\TestEmbl.java:18 Class seq.EmblFormat not found.
>             SequenceFormat eFormat = new EmblFormat();
> 
> seq\TestEmbl.java:21: Class seq.SimpleSequenceFactory not found.
>             SequenceFactory sFact = new SimpleSequenceFactory();
> 
> seq\TestEmbl.java:25: Incompatible type for constructor. Explicit cast needed to convert org.biojava.bio.seq.SequenceFactory to org.biojava.bio.seq.io.SequenceBuilderFactory.
>             new StreamReader(eReader, eFromat, rParser, sFact);
> 
> 3 errors
> */
> 
> Packages I downloaded from biojava site were
> bytecode-0.90.jar --> bytecode.jar (I renamed it as bytecode.jar)
> xerces.jar 
> jakarta-regexp.jar
> biojava-20010813.jar --> biojava.jar (I renamed it as biojara.jar)
> 
> Could kindly let me know what problem do I have and how can I solve it?