MatchImp Class Reference

#include <MatchStore.h>

Inheritance diagram for MatchImp:

[legend]Collaboration diagram for MatchImp:

[legend]List of all members.

Public Member Functions
virtual	~MatchImp ()
virtual SequenceNumber	getSubjectNum (void) const
virtual const char *	getSubjectName (void) const
virtual SequenceOffset	getSubjectStart (void) const
virtual SequenceOffset	getSubjectEnd (void) const
virtual SequenceNumber	getQueryNum (void) const
virtual string	getQueryName (void) const
virtual SequenceOffset	getQueryStart (void) const
virtual SequenceOffset	getQueryEnd (void) const
virtual int	getQuerySize (void) const
virtual int	getNumBases (void) const
virtual bool	isQueryForward (void) const
virtual bool	isSubjectForward (void) const
virtual void	print (void) const
	MatchImp (MatchStoreImp *myStore, SequenceNumber subjectNum, SequenceOffset numBases, SequenceOffset queryStart, SequenceOffset queryEnd, SequenceOffset subjectStart, SequenceOffset subjectEnd, bool isQueryForward, bool isSubjectForward)
Public Attributes
SequenceNumber	subjectNum_
SequenceOffset	numBases_
SequenceOffset	queryStart_
SequenceOffset	queryEnd_
SequenceOffset	subjectStart_
SequenceOffset	subjectEnd_
bool	isQueryForward_
bool	isSubjectForward_
MatchStoreImp *	myStore_

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Detailed Description

Definition at line 87 of file MatchStore.h.

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Constructor & Destructor Documentation

virtual MatchImp::~MatchImp

(

)

[inline, virtual]

Definition at line 91 of file MatchStore.h.

{}

MatchImp::MatchImp	(	MatchStoreImp *	myStore,
		SequenceNumber	subjectNum,
		SequenceOffset	numBases,
		SequenceOffset	queryStart,
		SequenceOffset	queryEnd,
		SequenceOffset	subjectStart,
		SequenceOffset	subjectEnd,
		bool	isQueryForward,
		bool	isSubjectForward
	)			[inline]

Definition at line 121 of file MatchStore.h.

                                    :
    myStore_( myStore ),
    subjectNum_( subjectNum ),  
    numBases_( numBases ),  
    queryStart_( queryStart ),
    queryEnd_( queryEnd ),
    subjectStart_( subjectStart ),
    subjectEnd_( subjectEnd ),
    isQueryForward_( isQueryForward ),
    isSubjectForward_( isSubjectForward ){}

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Member Function Documentation

virtual SequenceNumber MatchImp::getSubjectNum

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 93 of file MatchStore.h.

References subjectNum_.

    { return subjectNum_; }

const char * MatchImp::getSubjectName

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 43 of file MatchStore.cpp.

References NameReader::getSequenceName(), myStore_, MatchStoreImp::reader_, and subjectNum_.

{
  //  cout << "names_" << myStore_->names_.size() << endl; // %%%
  //  assert(myStore_->names_.find(subjectNum_)!=myStore_->names_.end());
  //  return myStore_->names_[ subjectNum_ ];

  return myStore_->reader_.getSequenceName(subjectNum_);

  //  string name;
  //  myStore_->subjectTable_.getSequenceName( name, subjectNum_ );
  //  return name;
}

Here is the call graph for this function:

virtual SequenceOffset MatchImp::getSubjectStart

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 97 of file MatchStore.h.

References subjectStart_.

    { return subjectStart_; }

virtual SequenceOffset MatchImp::getSubjectEnd

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 99 of file MatchStore.h.

References subjectEnd_.

    { return subjectEnd_; }

SequenceNumber MatchImp::getQueryNum

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 56 of file MatchStore.cpp.

References myStore_, and MatchStoreImp::queryNum_.

{
  return myStore_->queryNum_;
}

string MatchImp::getQueryName

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 61 of file MatchStore.cpp.

References myStore_, and MatchStoreImp::queryName_.

{
  return myStore_->queryName_;
}

virtual SequenceOffset MatchImp::getQueryStart

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 104 of file MatchStore.h.

References queryStart_.

    { return queryStart_; }

virtual SequenceOffset MatchImp::getQueryEnd

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 106 of file MatchStore.h.

References queryEnd_.

    { return queryEnd_; }

int MatchImp::getQuerySize

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 66 of file MatchStore.cpp.

References myStore_, and MatchStoreImp::queryBases_.

{
  return myStore_->queryBases_;
}

virtual int MatchImp::getNumBases

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 110 of file MatchStore.h.

References numBases_.

    { return numBases_; }

virtual bool MatchImp::isQueryForward

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 112 of file MatchStore.h.

References isQueryForward_.

    { return isQueryForward_; }

virtual bool MatchImp::isSubjectForward

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 114 of file MatchStore.h.

References isSubjectForward_.

    { return isSubjectForward_; }

virtual void MatchImp::print

(

void

)

const [inline, virtual]

Implements Match.

Definition at line 117 of file MatchStore.h.

{}

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Member Data Documentation

SequenceNumber MatchImp::subjectNum_

Definition at line 140 of file MatchStore.h.

Referenced by getSubjectName(), and getSubjectNum().

SequenceOffset MatchImp::numBases_

Definition at line 141 of file MatchStore.h.

Referenced by getNumBases().

SequenceOffset MatchImp::queryStart_

Definition at line 143 of file MatchStore.h.

Referenced by getQueryStart().

SequenceOffset MatchImp::queryEnd_

Definition at line 144 of file MatchStore.h.

Referenced by getQueryEnd().

SequenceOffset MatchImp::subjectStart_

Definition at line 145 of file MatchStore.h.

Referenced by getSubjectStart().

SequenceOffset MatchImp::subjectEnd_

Definition at line 146 of file MatchStore.h.

Referenced by getSubjectEnd().

bool MatchImp::isQueryForward_

Definition at line 148 of file MatchStore.h.

Referenced by isQueryForward().

bool MatchImp::isSubjectForward_

Definition at line 149 of file MatchStore.h.

Referenced by isSubjectForward().

MatchStoreImp* MatchImp::myStore_

Definition at line 151 of file MatchStore.h.

Referenced by getQueryName(), getQueryNum(), getQuerySize(), and 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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