MatchPolicyDNAProtein Class Reference

#include <QueryManager.h>

Inheritance diagram for MatchPolicyDNAProtein:

[legend]Collaboration diagram for MatchPolicyDNAProtein:

[legend]List of all members.

Public Member Functions
	MatchPolicyDNAProtein (HashTablePackedProtein &subjectTable)
virtual void	operator() (WordSequence &querySeqFwd, MatchStore &store, MatchAlgorithm &findMatch)
Protected Attributes
HashTablePackedProtein &	subjectTable_

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Detailed Description

Definition at line 284 of file QueryManager.h.

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Constructor & Destructor Documentation

MatchPolicyDNAProtein::MatchPolicyDNAProtein

(

HashTablePackedProtein &

subjectTable

)

Definition at line 228 of file QueryManager.cpp.

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

                                         :
MatchPolicy( subjectTable ),
subjectTable_( subjectTable )
{
  queryWordLength_ = gMaxBasesPerWord;
  subjectTable_.setQueryTranslatedDNA();

  addMatch_ = new MatchAdderCodonProtein(subjectTable_);

} // ~MatchPolicyDNAProtein::MatchPolicyDNAProtein

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Member Function Documentation

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

Implements MatchPolicy.

Definition at line 242 of file QueryManager.cpp.

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

{

  addMatch_->link(store);
  addMatch_->setQueryForward();

  addMatch_->setQuerySize( ((querySeqFwd.size()-1) * gMaxBasesPerWord )
      + querySeqFwd.getNumBasesInLast() );

  WordSequence querySeqRev;
  reverseComplement
    ( querySeqFwd, querySeqRev, 
      queryWordLength_ ); 

  //  cout << "MPDP: doing fwd" << endl;

  addMatch_->setQueryForward();

  findMatch( querySeqFwd, *addMatch_, subjectTable_,
             gNumReadingFrames * subjectTable_.getWordLength() ); 

  //  cout << "MPDP: doing rev" << endl;

  addMatch_->setQueryReverse();

  findMatch( querySeqRev, *addMatch_, subjectTable_,
             gNumReadingFrames * subjectTable_.getWordLength() );


} // ~void MatchPolicyDNAProtein::operator()

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Member Data Documentation

HashTablePackedProtein& MatchPolicyDNAProtein::subjectTable_ [protected]

Reimplemented from MatchPolicy.

Definition at line 295 of file QueryManager.h.

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The documentation for this class was generated from the following files:

• QueryManager/QueryManager.h
• QueryManager/QueryManager.cpp

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