MatchPolicyProteinTranslated Class Reference

#include <QueryManager.h>

Inheritance diagram for MatchPolicyProteinTranslated:

[legend]Collaboration diagram for MatchPolicyProteinTranslated:

[legend]List of all members.

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

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Detailed Description

Definition at line 312 of file QueryManager.h.

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Constructor & Destructor Documentation

MatchPolicyProteinTranslated::MatchPolicyProteinTranslated

(

HashTableTranslated &

subjectTable

)

Definition at line 278 of file QueryManager.cpp.

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

                                      :
MatchPolicy( subjectTable ),
subjectTable_( subjectTable )
{
  subjectTable_.setQueryProtein();
  addMatch_ = new MatchAdderProteinCodon(subjectTable_);
} // ~MatchPolicyProteinTranslated::MatchPolicyProteinTranslated

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Member Function Documentation

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

Implements MatchPolicy.

Definition at line 288 of file QueryManager.cpp.

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

{

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

  // Necessary to copy querySeqFwd - otherwise it is shifted by the
  // first findMatch, which thus screws up the second findMatch
  WordSequence querySeqCopy(querySeqFwd);

  //  addMatch_->setSubjectForward();
  //  cout << "MPPT: fwd" << endl;
  subjectTable_.setForward();

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

  //  addMatch_->setSubjectReverse();
  // cout << "MPPT: rev" << endl;
  subjectTable_.setReverse();

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


} // ~MatchPolicyProteinTranslated::operator()

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Member Data Documentation

HashTableTranslated& MatchPolicyProteinTranslated::subjectTable_ [protected]

Reimplemented from MatchPolicy.

Definition at line 323 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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