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

[Vasa Curcin]

Hi,

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:vc100 at doc.ic.ac.uk] 
>>Sent: Tuesday, 18 November 2003 11:28 p.m.
>>To: biojava-l at biojava.org
>>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
>>
>>_______________________________________________
>>Biojava-l mailing list  -  Biojava-l at biojava.org 
>>http://biojava.org/mailman/listinfo/biojava-l
>>
>>    
>>
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