[Biojava-l] Serialization of RemoteFeature.Region

2004-02-17 Thread Vasa Curcin
Hello, Serialization buff that I am, it's a wonder this one slipped past me earlier. RemoteFeature.Region won't serialize. Could this inner class be made serializable - some sequences obtained from Genbank won't serialize because of this. Cheers, Vasa

Re: [Biojava-l] Serialization of SequenceDB obtained from Swiss-Prot

2003-11-19 Thread Matthew Pocock
Message- From: Vasa Curcin [mailto:[EMAIL PROTECTED] Sent: Tuesday, 18 November 2003 11:28 p.m. To: [EMAIL PROTECTED] Subject: [Biojava-l] Serialization of SequenceDB obtained from Swiss-Prot Hello, There seems to be some problem with serializing SequenceDB objects obtained from SwissPro

Re: [Biojava-l] Serialization of SequenceDB obtained from Swiss-Prot

2003-11-19 Thread Vasa Curcin
t: Tuesday, 18 November 2003 11:28 p.m. To: [EMAIL PROTECTED] Subject: [Biojava-l] Serialization of SequenceDB obtained from Swiss-Prot Hello, There seems to be some problem with serializing SequenceDB objects obtained from SwissProtDatabase. The error is: java.io.WriteAbortedException: writi

RE: [Biojava-l] Serialization of SequenceDB obtained from Swiss-Prot

2003-11-18 Thread Schreiber, Mark
2003 11:28 p.m. > To: [EMAIL PROTECTED] > Subject: [Biojava-l] Serialization of SequenceDB obtained > from Swiss-Prot > > > Hello, > > There seems to be some problem with serializing SequenceDB objects > obtained from SwissProtDatabase. The error is: > >

[Biojava-l] Serialization of SequenceDB obtained from Swiss-Prot

2003-11-18 Thread Vasa Curcin
Hello, There seems to be some problem with serializing SequenceDB objects obtained from SwissProtDatabase. The error is: java.io.WriteAbortedException: writing aborted; java.io.NotSeria lizableException: org.biojava.bio.seq.io.SequenceBuilderBase$TemplateWithChildre n at java.io.ObjectI

RE: [Biojava-l] Serialization of SimpleSequences

2003-11-03 Thread Schreiber, Mark
mpl to hold its hand but hopefull not. - Mark -Original Message- From: Schreiber, Mark Sent: Tue 28/10/2003 3:40 p.m. To: Vasa Curcin; [EMAIL PROTECTED] Cc: Subject: RE: [Biojava-l] Serialization of SimpleSequences

RE: [Biojava-l] Serialization of SimpleSequences

2003-10-27 Thread Schreiber, Mark
f the implementations as possible serializable. I'll have a look at this. - Mark -Original Message- From: Vasa Curcin [mailto:[EMAIL PROTECTED] Sent: Tue 28/10/2003 2:06 p.m. To: [EMAIL PROTECTED] Cc: Subject: [Biojava-l] Serial

[Biojava-l] Serialization of SimpleSequences

2003-10-27 Thread Vasa Curcin
Hello, While transferring some sequences via serialization, I noticed that all my Features are getting lost. After some digging around, it seems as if Java doesn't serialize the FeatureHolder inside the sequence (I was working with SimpleSequence objects). Even though a NotSerializableExceptio

Re: [Biojava-l] Serialization involving NameTokenization

2002-10-13 Thread Matthew Pocock
Objections? Matthew > > > >>-Original Message- >>From: Lachlan Coin [mailto:[EMAIL PROTECTED]] >>Sent: Friday, 11 October 2002 1:48 a.m. >>To: [EMAIL PROTECTED] >>Subject: [Biojava-l] Serialization involving NameTokenization >&g

RE: [Biojava-l] Serialization involving NameTokenization

2002-10-10 Thread Schreiber, Mark
ges to the BioJava live branch. - Mark > -Original Message- > From: Lachlan Coin [mailto:[EMAIL PROTECTED]] > Sent: Friday, 11 October 2002 1:48 a.m. > To: [EMAIL PROTECTED] > Subject: [Biojava-l] Serialization involving NameTokenization > > > Hi, > >

[Biojava-l] Serialization involving NameTokenization

2002-10-10 Thread Lachlan Coin
Hi, I'm trying to serialize something which contains an alphabet and hence a NameTokenization. However, NameTokenization is not serializable. Any ideas how to get around this? Thanks very much, Lachlan ___ Biojava-l mailing list - [EMAIL PROTECTE

Re: [Biojava-l] Serialization and 1.2

2002-01-22 Thread Thomas Down
On Tue, Jan 22, 2002 at 03:33:54PM +1300, Schreiber, Mark wrote: > > A while ago there was some discussion of serialization of biojava > objects and the problems of rebuilding things like alphabet indexer. Is > it a realistic goal to get this up and running with some jUnit tests for > biojava 1.2

[Biojava-l] Serialization and 1.2

2002-01-21 Thread Schreiber, Mark
Hi - A while ago there was some discussion of serialization of biojava objects and the problems of rebuilding things like alphabet indexer. Is it a realistic goal to get this up and running with some jUnit tests for biojava 1.2? I wouldn't mind helping (due to considerable self interest in this)

[Biojava-l] serialization of HashSequenceDB

2001-07-04 Thread Mark Schreiber
Hi - When trying to serialize a HashSequenceDB I get the following error trace, java.lang.NoSuchFieldException at java.lang.Class.getField0(Native Method) at java.lang.Class.getField(Class.java:826) at org.biojava.bio.seq.impl.FeatureImpl$1.writeReplace(FeatureImpl.java:5

Re: [Biojava-l] serialization

2001-05-11 Thread Matthew Pocock
This should be fine for short-term (ie RMI) applications. I would advise against it for any resource you want stored between updating your biojava.jar release as serialization may be broken between them. One option is to use XML beans as your serialization format which should be more forgiving

[Biojava-l] serialization

2001-05-09 Thread Schreiber, Mark
Hi - I think this question was asked a while ago but I don't recall the final consensus so here goes... Is it a good idea to store a bunch of sequences by serializing a HashSequenceDB? If not what would be a better way? Mark Mark Schreiber Bioinformatics AgResearch Invermay PO Box 50034 Mosg