Hi Bernd:
I am having this need too. Have you been able to serialize properly
SimpleRichSequence? Is-it possible for you to share you code? We could
add it to BioJava. Let me know.
Thanks,
George
------------------------------------------------------------------------------
On Mon, Sep 27, 2010 at 6:17 AM, Bernd Jagla <[email protected]> wrote:
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/
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
_______________________________________________
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