MatchAlgorithm Class Reference

#include <MatchStoreGapped.h>

Inheritance diagram for MatchAlgorithm:


Public Member Functions
	MatchAlgorithm (int numRepeats)
void	operator() (WordSequence &querySeq, MatchAdder &addMatch, HashTableGeneric &subjectTable, int wordLength=-1, int stepLength=-1)
void	generateHits (WordSequence &querySeq, HitListVector &hitList, HashTableGeneric &subjectTable)
virtual void	generateMatches (HitListVector &hitList, MatchAdder &addMatch)=0
Protected Attributes
bool	sortNeeded_
int	numRepeats_
int	wordLength_
int	stepLength_

Detailed Description

Definition at line 56 of file MatchStoreGapped.h.

Constructor & Destructor Documentation

MatchAlgorithm::MatchAlgorithm ( int numRepeats ) [inline]

Definition at line 59 of file MatchStoreGapped.h.

00059                                    : 
00060     numRepeats_( numRepeats ), sortNeeded_(true) {}

Member Function Documentation

void MatchAlgorithm::operator()	(	WordSequence &	querySeq,
		MatchAdder &	addMatch,
		HashTableGeneric &	subjectTable,
		int	wordLength = `-1`,
		int	stepLength = `-1`
	)

Definition at line 50 of file MatchStoreGapped.cpp.

References wordLength.

00055 {
00056   //  cout << "MatchAlgorithm()" << endl;
00057   HitListVector hitList;
00058   wordLength_ = ((wordLength==-1)?subjectTable.getWordLength():wordLength);
00059   stepLength_ = ((stepLength==-1)?wordLength_:stepLength);
00060   assert(hitList.size()==0);
00061 
00062   if (dynamic_cast<HashTablePacked*>(&subjectTable)!=NULL)
00063   {
00064     sortNeeded_ = false;
00065   } // ~if
00066 
00067   generateHits( querySeq, hitList, subjectTable );
00068   //  cout << "MatchAlgorithm() - hits got: " << hitList.size() << endl;
00069   generateMatches( hitList, addMatch );
00070 }

void MatchAlgorithm::generateHits	(	WordSequence &	querySeq,
		HitListVector &	hitList,
		HashTableGeneric &	subjectTable
	)

Definition at line 73 of file MatchStoreGapped.cpp.

References HashTableGeneric::matchSequence(), and HashTableGeneric::setNumRepeats().

00074 {
00075   subjectTable.setNumRepeats( numRepeats_ );
00076   //  wordLength_ = subjectTable.getWordLength();
00077   //  stepLength_ = subjectTable.getStepLength();
00078   subjectTable.matchSequence( querySeq, hitList );
00079 }

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