I am still investigating when exactly the problem with writing out the object occurs, but this may be related. Here, I am returning matches from a SwissProt search from the server to the client. The object is a SequenceDB obtained from SwissProt and the entry has the following line:
FT INIT_MET 0 0 BY SIMILARITY.
This is the exact exception:
17:32:29,654 ERROR [STDERR] got data from http://us.expasy.org/cgi-bin/get-sprot
-raw.pl?143B_MOUSE
17:32:30,605 ERROR [STDERR] java.lang.IllegalArgumentException: Location 0 is ou
tside 1..245
at org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:306)
at sun.reflect.GeneratedConstructorAccessor85.newInstance(Unknown Source
)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingC
onstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:274)
at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(Simple
FeatureRealizer.java:138)
rethrown as org.biojava.bio.BioException: Couldn't realize feature
at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(Simple
FeatureRealizer.java:144)
at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatur
eRealizer.java:94)
at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence
.java:198)
at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.
java:204)
at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuild
erBase.java:168)
at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenc
eBuilder.java:87)
at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBui
lderFilter.java:98)
at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:10
1)
at org.biojava.bio.seq.db.SwissprotSequenceDB.getSequence(SwissprotSeque
nceDB.java:93)
Is this 0, 0 location common in Swiss-Prot entries? It seems the serialization is failing only on those entries which have this feature.
Regards, Vasa
Schreiber, Mark wrote:
Hi -
I'm not sure serializing an entire SequenceDB is a good idea, however, can you tell me if the serialization is failing on the DB or one of the sequences in it?
- Mark
-----Original 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 SwissProtDatabase. The error is:
java.io.WriteAbortedException: writing aborted; java.io.NotSeria
lizableException: org.biojava.bio.seq.io.SequenceBuilderBase$TemplateWithChildre
n
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1278)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:324)
at java.util.HashSet.readObject(HashSet.java:272)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
I am using Biojava 1.30, with Mark's patches from a few weeks back. Anyone has an idea?
Regards, Vasa
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