[BiO BB] BLAST with multiple queries

Dr. Christoph Gille christoph.gille at charite.de
Mon Dec 19 21:07:26 EST 2005

>From recent posts I learned that modern BLAST implementations
might be faster if many queries  are processed simultaneously
since the database is scanned only once.

I wonder whether I should take this into account in the Java API
and would like to ask you for your opinion.

The disadvantage would be that the programming interface would become more
difficult even though most users will not use this modern feature of
multiple sequences.

There would be some changes necessary: I would need to turn
setAAQuerySequence(String s) into setAAQuerySequences(String[] ss)

In the same way I would need to change getQuerySequence() and
setNTQuerySequence(String s) into plural.

The blast result would be retrieved giving the result number as parameter:
 String 	getResultXml(int number)

Currently I delete the cache entry by CacheResult.remove(SequenceBlaster)

For this purpose I would need to make a new instance method, something like
SequenceBlaster#removeInCache(int resultNumber);

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