MatchAdderProteinCodon Class Reference

#include <QueryManager.h>

Inheritance diagram for MatchAdderProteinCodon:

[legend]Collaboration diagram for MatchAdderProteinCodon:

[legend]List of all members.

Public Member Functions
	MatchAdderProteinCodon (HashTableTranslated &subjectTable)
virtual void	operator() (SequenceNumber subjectNum, SequenceOffset numBases, SequenceOffset queryStart, SequenceOffset queryEnd, SequenceOffset subjectStart, SequenceOffset subjectEnd)
Private Attributes
SequenceOffset	size_
HashTableTranslated &	subjectTable_

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Detailed Description

Definition at line 205 of file QueryManager.h.

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Constructor & Destructor Documentation

MatchAdderProteinCodon::MatchAdderProteinCodon

(

HashTableTranslated &

subjectTable

)

Definition at line 72 of file QueryManager.cpp.

                                                                                  :
MatchAdderImp( subjectTable ), subjectTable_( subjectTable ) {}

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Member Function Documentation

void MatchAdderProteinCodon::operator()	(	SequenceNumber	subjectNum,
		SequenceOffset	numBases,
		SequenceOffset	queryStart,
		SequenceOffset	queryEnd,
		SequenceOffset	subjectStart,
		SequenceOffset	subjectEnd
	)			[virtual]

Reimplemented from MatchAdderImp.

Definition at line 127 of file QueryManager.cpp.

References MatchStore::addMatch(), HashTableGeneric::getSequenceSize(), gNumReadingFrames, HashTableTranslated::isForward(), MatchAdderImp::lastSubjectNum_, MatchAdder::pStore_, size_, and subjectTable_.

{


  if (subjectNum!=lastSubjectNum_)
  {
    //    subjectTable_.getSequenceName(name_,subjectNum);
    size_ = subjectTable_.getSequenceSize(subjectNum);
    lastSubjectNum_=subjectNum;
  } // ~if

  //  cout << "MAPC: " << subjectNum << " " << queryStart << " " << queryEnd
  //   << " " << subjectStart << " " << subjectEnd << " - " << size_ << endl;

  pStore_->addMatch( // name_,
                     subjectNum, 
                     numBases/gNumReadingFrames, 
                     (queryStart+2)/gNumReadingFrames,  
                     queryEnd/gNumReadingFrames, 
                     //                              subjectStart,
                     //   subjectEnd,
                     subjectTable_.isForward() ? subjectStart
                     : size_ - subjectEnd + 1,
                     subjectTable_.isForward() ? subjectEnd
                     : size_ - subjectStart + 1, 
                     true,
                     subjectTable_.isForward() );
                     
} // ~MatchAdderProteinCodon::operator()

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Member Data Documentation

SequenceOffset MatchAdderProteinCodon::size_ [private]

Definition at line 216 of file QueryManager.h.

Referenced by operator()().

HashTableTranslated& MatchAdderProteinCodon::subjectTable_ [private]

Reimplemented from MatchAdder.

Definition at line 217 of file QueryManager.h.

Referenced by operator()().

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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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