ssaha: MatchPolicyDNADNA Class Reference

MatchPolicyDNADNA::MatchPolicyDNADNA ( HashTableGeneric & subjectTable )

Definition at line 172 of file QueryManager.cpp.

References MatchPolicy::addMatch_, and MatchPolicy::subjectTable_.

Referenced by QueryManager::QueryManager().

00172                                                                      :
00173 MatchPolicy( subjectTable )
00174 {
00175  addMatch_ = new MatchAdderImp(subjectTable_); 
00176 }

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void MatchPolicyDNADNA::operator()	(	WordSequence &	querySeqFwd,
		MatchStore &	store,
		MatchAlgorithm &	findMatch
	)			`[virtual]`

Implements MatchPolicy.

Definition at line 180 of file QueryManager.cpp.

References MatchPolicy::addMatch_, WordSequence::getNumBasesInLast(), HashTableGeneric::getWordLength(), MatchAdder::link(), MatchPolicy::queryWordLength_, reverseComplement(), MatchAdder::setQueryForward(), MatchAdder::setQueryReverse(), MatchAdder::setQuerySize(), and MatchPolicy::subjectTable_.

00182 {
00183 
00184   addMatch_->link(store);
00185   addMatch_->setQuerySize( ((querySeqFwd.size()-1) * queryWordLength_ )
00186       + querySeqFwd.getNumBasesInLast() );
00187 
00188   WordSequence querySeqRev;
00189   reverseComplement
00190     ( querySeqFwd, querySeqRev, 
00191       subjectTable_.getWordLength() ); 
00192 
00193   addMatch_->setQueryForward();
00194 
00195   findMatch( querySeqFwd, *addMatch_, subjectTable_ ); 
00196 
00197   addMatch_->setQueryReverse();
00198 
00199   findMatch( querySeqRev, *addMatch_, subjectTable_ );
00200 
00201 } // ~QueryManager::doMatch

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Public Member Functions
	MatchPolicyDNADNA (HashTableGeneric &subjectTable)
virtual void	operator() (WordSequence &querySeqFwd, MatchStore &store, MatchAlgorithm &findMatch)

MatchPolicyDNADNA Class Reference

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation