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

[Matthew Pocock]

I think the sp parser needs to special-case this - the location is meant 
to have the semantics of being 'before' the sequence starts (I think). 
Could someone brave fix this special case in the SP parser? Perhaps a 
fuzzy range, with both < 1? Also the sp file writer will need modifying 
to round-trip this.

Grr.

Matthew

Vasa Curcin wrote:

> 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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>
>
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