[Biojava-dev] MappedDataStoreFactory bug

[Schreiber, Mark]

Using the CompactedDataStoreFactory doesn't have this problem.

	-----Original Message----- 
	From: Thomas Down [mailto:td2 at sanger.ac.uk] 
	Sent: Wed 23/04/2003 10:23 p.m. 
	To: Schreiber, Mark 
	Cc: biojava-dev at biojava.org 
	Subject: Re: [Biojava-dev] MappedDataStoreFactory bug
	
	

	On Wed, Apr 23, 2003 at 04:32:49PM +1200, Schreiber, Mark 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);
	
	Could you send me the script you're using?  A quick read through
	PackingFactory looks okay to me.
	
	The one case I can see which will cause breakage is if you use a
	Packing which returns an out-of-range value to indicate ambiguity
	symbols (which is really useful if you want to simply exclude runs
	of 'N's from your table).  The alternative implementation,
	CompactedDataStoreFactory, *does* handle this usage (but
	it's written in a rather different way and doesn't use the
	PackingFactory methods).
	
	Is this what you're trying?
	
	Unless you need to index very large abouts of sequence, I'd
	actually encourage the use of CompactedDataStoreFactory, since
	it can save a lot of disk space without hurting performance too
	much.
	
	     Thomas.
	
	


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