[Biojava-l] new problem: serializable

[Richard Holland]

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
http://www.eaglegenomics.com/