[Biojava-l] new problem: serializable

[Richard Holland]

I think you can follow James' advice and subclass SimpleRichSequence, and then annotate it such that the awkward bits are not seralised.

Or, you can just extract the parameters of interest out of the original object and put them into some holding class (e.g. a simple HashMap) as I suggested and serialise that instead.

cheers,
Richard

On 27 Sep 2010, at 13:01, Bernd Jagla wrote:

> Thanks everyone. I got the biojavax working.
> Unfortunately the serialization process is not completely done yet ...
> It turns out the following information is more difficult than expected to serialize... I haven't found a tool in Eclipse that can help me there.
> 
> Generally the problems arise when dealing with Sets like annotation, features, notes, RankedDocRef. 
> But I also have problems with SimpleNCBITaxon.
> 
> At least I was able to create a SimpleRichSequence object
> 
> Please let me know if you can think of something that would ease the work a bit....
> 
> Thanks a lot,
> 
> Bernd
> 
> 
> 
> On 9/23/2010 6:01 PM, James Swetnam wrote:
>> How about subclassing SimpleRichSequence and implementing serializable yourself?  Doesn't seem to be final.  Eclipse can do it in a jiffy.  Hacky, but will get you over the bump.
>> 
>> James Swetnam
>> 
>> On Thu, Sep 23, 2010 at 11:34 AM, Richard Holland <holland at eaglegenomics.com> wrote:
>> The RichSequence interface doesn't extend Serializable, so therefore you can't seralize BioJavaX sequence objects. :( I can't remember the logic behind that one but it seemed like there was a good reason at the time...
>> 
>> If you're passing sequences around by serialisation, do you really need to pass the complete object or could you just pass the bits you're interested in in some kind of basic data structure?
>> 
>> 
>> On 23 Sep 2010, at 16:27, Bernd Jagla wrote:
>> 
>> > Sorry, again me...
>> >
>> > I now get the following error:
>> >
>> > Caused by: java.io.NotSerializableException: org.biojavax.bio.seq.SimpleRichSequence
>> >    at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1156)
>> >    at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1509)
>> >    at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1474)
>> >    at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1392)
>> >    at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1150)
>> >    at java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:326)
>> >    at org.knime.core.data.container.DCObjectOutputVersion2.writeDataCellPerJavaSerialization(DCObjectOutputVersion2.java:127)
>> >    at org.knime.core.data.container.Buffer.writeBlobDataCell(Buffer.java:1253)
>> >    at org.knime.core.data.container.Buffer.handleIncomingBlob(Buffer.java:790)
>> >    at org.knime.core.data.container.Buffer.saveBlobs(Buffer.java:607)
>> >    at org.knime.core.data.container.Buffer.addRow(Buffer.java:551)
>> >    ... 9 more
>> >
>> > It seems that the SimpleRichSequence is not serializable....
>> >
>> > Is there a way to make use of a serializable object?
>> >
>> > Thanks,
>> >
>> > Bernd
>> >
>> > _______________________________________________
>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> --
>> Richard Holland, BSc MBCS
>> Operations and Delivery Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>> http://www.eaglegenomics.com/
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> 
>> 
>> -- 
>> James Swetnam
>> Lead Scientific Programmer
>> Department of Pharmacology
>> NYU Langone Medical Center
>> 

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/