[Biojava-l] new problem: serializable

[Bernd Jagla]

  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 <mailto: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
>     >
>     > _______________________________________________
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>
>     --
>     Richard Holland, BSc MBCS
>     Operations and Delivery Director, Eagle Genomics Ltd
>     T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>     <mailto:holland at eaglegenomics.com>
>     http://www.eaglegenomics.com/
>
>
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>
>
>
> -- 
> James Swetnam
> Lead Scientific Programmer
> Department of Pharmacology
> NYU Langone Medical Center
>