#include <QueryManager.h>
Inheritance diagram for MatchPolicyDNATranslated:
Public Member Functions | |
| MatchPolicyDNATranslated (HashTableTranslated &subjectTable) | |
| virtual void | operator() (WordSequence &querySeqFwd, MatchStore &store, MatchAlgorithm &findMatch) |
Protected Attributes | |
| HashTableTranslated & | subjectTable_ |
Definition at line 298 of file QueryManager.h.
| MatchPolicyDNATranslated::MatchPolicyDNATranslated | ( | HashTableTranslated & | subjectTable | ) |
Definition at line 321 of file QueryManager.cpp.
References MatchPolicy::addMatch_, gMaxBasesPerWord, MatchPolicy::queryWordLength_, and MatchPolicy::subjectTable_.
00321 : 00322 MatchPolicy( subjectTable ), 00323 subjectTable_( subjectTable ) 00324 { 00325 queryWordLength_ = gMaxBasesPerWord; 00326 subjectTable_.setQueryTranslatedDNA(); 00327 addMatch_ = new MatchAdderCodonCodon(subjectTable_); 00328 // addMatch_ = new MatchAdderImp(subjectTable_); 00329 } // ~MatchPolicyDNATranslated::MatchPolicyDNATranslated
| void MatchPolicyDNATranslated::operator() | ( | WordSequence & | querySeqFwd, | |
| MatchStore & | store, | |||
| MatchAlgorithm & | findMatch | |||
| ) | [virtual] |
Implements MatchPolicy.
Definition at line 335 of file QueryManager.cpp.
References MatchPolicy::addMatch_, WordSequence::getNumBasesInLast(), HashTableGeneric::getWordLength(), gMaxBasesPerWord, gNumReadingFrames, MatchAdder::link(), reverseComplement(), MatchAdder::setQueryForward(), MatchAdder::setQueryReverse(), MatchAdder::setQuerySize(), and MatchPolicy::subjectTable_.
00337 { 00338 00339 addMatch_->link(store); 00340 00341 addMatch_->setQuerySize( ((querySeqFwd.size()-1) * gMaxBasesPerWord ) 00342 + querySeqFwd.getNumBasesInLast() ); 00343 00344 WordSequence revSeq, translatedQuery; 00345 00346 reverseComplement( querySeqFwd, revSeq, gMaxBasesPerWord ); 00347 00348 addMatch_->setQueryForward(); 00349 00350 // addMatch_->setSubjectForward(); 00351 subjectTable_.setForward(); 00352 00353 findMatch( querySeqFwd, *addMatch_, subjectTable_, 00354 gNumReadingFrames * subjectTable_.getWordLength() ); 00355 00356 // addMatch_->setSubjectReverse(); 00357 subjectTable_.setReverse(); 00358 00359 findMatch( querySeqFwd, *addMatch_, subjectTable_, 00360 gNumReadingFrames * subjectTable_.getWordLength() ); 00361 00362 addMatch_->setQueryReverse(); 00363 00364 // addMatch_->setSubjectForward(); 00365 subjectTable_.setForward(); 00366 00367 findMatch( revSeq, *addMatch_, subjectTable_, 00368 gNumReadingFrames * subjectTable_.getWordLength() ); 00369 00370 // addMatch_->setSubjectReverse(); 00371 subjectTable_.setReverse(); 00372 00373 findMatch( revSeq, *addMatch_, subjectTable_, 00374 gNumReadingFrames * subjectTable_.getWordLength() ); 00375 00376 00377 00378 } // ~MatchPolicyDNATranslated::operator()
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1.5.2