[Biojava-l] new problem: serializable

[James Swetnam]

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