[Biojava-l] sequence similarity searches - some code

Thu, 29 Jun 2000 19:57:09 +0200

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hi!

Since the topic of BLAST-parsing was mentioned again in an earlier mail,
i thought i could share with you an object-model for sequence-similarity
searches that i've developed over the last few days.

The object-model is defined through interfaces and should be able to
handle all kinds of sequence similarity searches, including BLAST.
Please look in this order at:
	SeqSimilaritySearcher
	SeqSimilaritySearchResult
	SeqSimilaritySearchHit
	SeqSimilaritySearchSubHit

Simple (but sufficient) implementations for result, hit and sub-hit can
be found in these classes, but they don't really contain any
intelligence:
	SimpleSeqSimilaritySearchResult
	SimpleSeqSimilaritySearchHit
	SimpleSeqSimilaritySearchSubHit

An abstract super-class of concrete implementations of a sequence
similarity searcher is
	AbstractSeqSimilaritySearcher
This class handles many things that should be common to all searchers
like configuration from a Java property file and launching the actual
search process and handling input and output to it. It delegates to
abstract methods (following the Template Method Pattern) that need to be
implemented by the concrete sub-classes of this class.

Class
	NCBIBlastPSearcher
and the property file
	ncbi_blastp_searcher.properties
is a partly finished concrete parser for the NCBI BLASTP implementation.
The hard parsing part, namely parsing the alignments from the textual
output of BLASTP still needs to be done...

The whole design lacks many of the sexy aspects of the XML-SAX-based
parser that has been proposed some time ago on this list but i think
that the object-model (defined through the interfaces) describes pretty
accurately how we think of sequence similarity searches - and this was
important to me. Furthermore, it's straightforward to use once
implemented - look at NCBIBlastPSearcher.main().

Please look at the code of at least the interfaces
(SeqSimilaritySearcher, SeqSimilaritySearchResult,
SeqSimilaritySearchHit, SeqSimilaritySearchSubHit) and let me know what
you think of it and what the place of this within BioJava could be!

(you won't be able to compile any of this because it lives within my
package tree and depends on other classes which i don't want to go into
the trouble to send now...)

	cheers,
	gerald
-- 
   Gerald.Loeffler@vienna.at _________________ Software Architect
   http://www.imp.univie.ac.at ____ http://www.daemonstration.com
   OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
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Content-Type: application/x-unknown-content-type-java_auto_file;
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Content-Type: application/x-unknown-content-type-java_auto_file;
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Content-Disposition: inline;
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