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] > 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 - [email protected] > > 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: [email protected] > http://www.eaglegenomics.com/ > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- James Swetnam Lead Scientific Programmer Department of Pharmacology NYU Langone Medical Center _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
