[Biojava-dev] MappedDataStoreFactory bug

[Matthew Pocock]

Hi Mark,

10 is an odd number for it to fail on. 15 or 16 would
make sence (32 bits, signed integers). Can you run
your app and get it to print out this first word,
along with the number of elements in the hash table?
The packing code looks good to me, but then I never
was much good with binary.

Matthew

 --- "Schreiber, Mark"
<mark.schreiber at agresearch.co.nz> wrote: > Hi -
>  
> When trying to increase the wordLength argument of 
> MappedDataStoreFactory.buildDataStore() above 10 I
> get an index out of bounds exception
>  
> Exception in thread "main"
> java.lang.IndexOutOfBoundsException
>         at
> java.nio.Buffer.checkIndex(Buffer.java:438)
>         at
>
java.nio.ByteBufferAsIntBufferB.get(ByteBufferAsIntBufferB.java:96)
>         at
>
org.biojava.bio.program.ssaha.MappedDataStoreFactory.addCount(MappedDataStoreFactory.java:305)
>         at
>
org.biojava.bio.program.ssaha.MappedDataStoreFactory.buildDataStore(MappedDataStoreFactory.java:143)
>         at
>
ssaha.CreateDNAFastaHashTable.main(CreateDNAFastaHashTable.java:31)
>  
> I think this might be caused by an innapropriate
> value for "word" created by this statement on line
> 141
>  
> int word = PackingFactory.primeWord(seq, wordLength,
> packing);
>  
> Can anyone help?
>  
> - Mark
> 
>
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