Yes, that's what I am doing. I have subclassed from SimpleRichSequence
to SimpleSerializableRichSequence (couldn't think of something nicer...)
and am working my way through the bits...
I just haven't found the tools that make this a "jiffy". I am sweating
here; more or less at least.. ;)
Thanks again
B
On 9/27/2010 2:04 PM, Richard Holland wrote:
I think you can follow James' advice and subclass SimpleRichSequence, and then
annotate it such that the awkward bits are not seralised.
Or, you can just extract the parameters of interest out of the original object
and put them into some holding class (e.g. a simple HashMap) as I suggested and
serialise that instead.
cheers,
Richard
On 27 Sep 2010, at 13:01, Bernd Jagla wrote:
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]>
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]
http://www.eaglegenomics.com/
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--
James Swetnam
Lead Scientific Programmer
Department of Pharmacology
NYU Langone Medical Center
--
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/
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