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
<[email protected] <mailto:[email protected]>> 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: [email protected]
<mailto:[email protected]>
http://www.eaglegenomics.com/
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--
James Swetnam
Lead Scientific Programmer
Department of Pharmacology
NYU Langone Medical Center
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