MatchStoreImp Class Reference

#include <MatchStore.h>

Inheritance diagram for MatchStoreImp:

[legend]Collaboration diagram for MatchStoreImp:

[legend]List of all members.

Public Member Functions
	MatchStoreImp (string queryName, int queryNum, int queryBases, const NameReader &reader)
	~MatchStoreImp ()
virtual void	addMatch (SequenceNumber subjectNum, SequenceOffset numBases, SequenceOffset queryStart, SequenceOffset queryEnd, SequenceOffset subjectStart, SequenceOffset subjectEnd, bool isQueryForward, bool isSubjectForward)
void	printResult (ostream &outputStream=cout) const
virtual void	clear (void)
void	setup (void)
Protected Attributes
vector< MatchImp * >	imps_
string	queryName_
int	queryNum_
int	queryBases_
const NameReader &	reader_
Friends
class	MatchImp

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Detailed Description

Definition at line 181 of file MatchStore.h.

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Constructor & Destructor Documentation

MatchStoreImp::MatchStoreImp	(	string	queryName,
		int	queryNum,
		int	queryBases,
		const NameReader &	reader
	)			[inline]

Definition at line 185 of file MatchStore.h.

                                           :
  queryName_ ( queryName ),
  queryNum_( queryNum ),
  queryBases_( queryBases ), 
  reader_( reader )
    {
      //      reserve(1000);
      //     imps_.reserve(1000);
    }

MatchStoreImp::~MatchStoreImp

(

)

Definition at line 110 of file MatchStore.cpp.

References imps_.

{
  for (vector<MatchImp*>::iterator i(imps_.begin()) ; i!= imps_.end() ; ++i )
    delete (*i);

}

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Member Function Documentation

void MatchStoreImp::addMatch	(	SequenceNumber	subjectNum,
		SequenceOffset	numBases,
		SequenceOffset	queryStart,
		SequenceOffset	queryEnd,
		SequenceOffset	subjectStart,
		SequenceOffset	subjectEnd,
		bool	isQueryForward,
		bool	isSubjectForward
	)			[virtual]

Reimplemented from MatchStore.

Definition at line 131 of file MatchStore.cpp.

References DEBUG_L2, and imps_.

{
  DEBUG_L2(             subjectNum << " " << 
                        numBases << " " << 
                        queryStart << " " << 
                        queryEnd << " " << 
                        subjectStart << " " << 
                        subjectEnd << " " << 
                        isQueryForward );

  imps_.push_back( new MatchImp ( this,
                                  subjectNum, 
                                  numBases, 
                                  queryStart, 
                                  queryEnd, 
                                  subjectStart, 
                                  subjectEnd, 
                                  isQueryForward,
                                  isSubjectForward) );
  //  push_back(static_cast<Match*>(imps_.back()));
  //  names_.insert(pair<SequenceNumber, string>(subjectNum, subjectName));
  //  cout << "inserting subject num" << subjectNum << " " << subjectName
  //     << endl;
  //  push_back(&matchImps_.back());
  //  MatchStore::iterator i(&back());
  //  DEBUG_L1( matchImps_.size() << " " << size() << " " 
  //    << i << " " << *i << " "  );
  //  DEBUG_L1( (*i)->getQueryNum() << " " << (*i)->getQueryName() << " " 
  //    << (*i)->getQueryStart() << " " << (*i)->getQueryEnd() << " " 
  //    << (*i)->getSubjectNum() << " " << (*i)->getSubjectName() << " " 
  //    << (*i)->getSubjectStart() << " " << (*i)->getSubjectEnd() ); 
  

}

void MatchStoreImp::printResult

(

ostream &

outputStream = cout

)

const [virtual]

Reimplemented from MatchStore.

Definition at line 79 of file MatchStore.cpp.

{ 
  
  if (empty()) return;

  outputStream << endl << "Matches For Query " 
               << queryNum_
               << " (" << queryBases_
               << " bases): " << queryName_
               << "\n\n";    
 
  for( vector<MatchImp*>::const_iterator i(imps_.begin());i!=imps_.end();++i)
  {
    //    MatchImp* i(*j);

    outputStream << (((*i)->isQueryForward_)?"F":"R")
                 <<" " << (*i)->subjectNum_
                 << "\t: " << (*i)->getSubjectName()// names_[(*i)->subjectNum_]
                 << "\tBases: " << (*i)->numBases_
                 << "\tQ: " << (*i)->queryStart_ 
                 << " to " << (*i)->queryEnd_
                 << "\tS: " << (*i)->subjectStart_ 
                 << " to " << (*i)->subjectEnd_ 
                 << "\n"; 

  }  // ~for i
   
  outputStream << endl;

} // ~QueryManager::printResult

void MatchStoreImp::clear

(

void

)

[virtual]

Reimplemented from MatchStore.

Definition at line 117 of file MatchStore.cpp.

References imps_, and queryBases_.

{ 
    
  for (vector<MatchImp*>::iterator i(imps_.begin()) ; i!= imps_.end() ; ++i )
    delete (*i);
  vector<Match*>::clear();
  imps_.clear();
  //    matchImps_.clear();
  queryBases_ = 0;
}

void MatchStoreImp::setup

(

void

)

Definition at line 174 of file MatchStore.cpp.

References imps_.

{
  vector<Match*>::clear();
  for ( vector<MatchImp*>::iterator i(imps_.begin());i!=imps_.end();++i)
    push_back( static_cast<Match*>(*i));
}

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Friends And Related Function Documentation

friend class MatchImp [friend]

Definition at line 183 of file MatchStore.h.

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Member Data Documentation

vector<MatchImp*> MatchStoreImp::imps_ [protected]

Definition at line 221 of file MatchStore.h.

Referenced by addMatch(), clear(), setup(), and ~MatchStoreImp().

string MatchStoreImp::queryName_ [protected]

Definition at line 223 of file MatchStore.h.

Referenced by MatchImp::getQueryName().

int MatchStoreImp::queryNum_ [protected]

Definition at line 224 of file MatchStore.h.

Referenced by MatchImp::getQueryNum().

int MatchStoreImp::queryBases_ [protected]

Definition at line 225 of file MatchStore.h.

Referenced by clear(), and MatchImp::getQuerySize().

const NameReader& MatchStoreImp::reader_ [protected]

Definition at line 228 of file MatchStore.h.

Referenced by MatchImp::getSubjectName().

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

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

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