HashTableTranslated Class Reference

#include <HashTableTranslated.h>

Inheritance diagram for HashTableTranslated:

[legend]Collaboration diagram for HashTableTranslated:

[legend]List of all members.

Public Types
enum	{ eDNAWordSizeForHashing = gMaxBasesPerWord-1 }
typedef void(HashTableTranslated::*)	MatchSequencePointer (WordSequence &, HitList &)
Public Member Functions
	HashTableTranslated (ostream &monitoringStream=cerr, string name="", Allocator< PositionPacked > &hitListAllocator=HashTablePacked::defaultHitListAllocator, Allocator< PositionInHitList > &arrayAllocator=HashTablePacked::defaultArrayAllocator)
virtual	~HashTableTranslated ()
virtual void	loadHashTable (SourceReaderIndex *pSourceReader=NULL)
virtual void	saveHashTable (void)
virtual void	setupPointerArray (void)
virtual int	countWordsAndGetNames (SequenceReader &sequenceReader, SequenceAdapter *seq)
virtual void	computePointerArray (void)
virtual void	setupHitList (void)
virtual void	hashAllWords (SequenceReader &sequenceReader, SequenceAdapter *seq, int numSeqs)
virtual void	cleanupTempData (void)
virtual void	hashWords (SequenceAdapter &thisSeq, SequenceNumber seqNum)
virtual void	countWords (SequenceAdapter &thisSeq)
virtual void	matchSequence (WordSequence &seq, HitList &hitListFwd)
void	matchSequenceProtein (WordSequence &seq, HitList &hitListFwd)
void	matchSequenceTranslatedDNA (WordSequence &seq, HitList &hitListFwd)
virtual void	setNumRepeats (int nr)
virtual void	setSubstituteThreshold (int ns)
virtual char *	getHitListStart (void) const
virtual int	getHitTypeSize (void) const
virtual void	allocateHitList (unsigned long size)
virtual void	loadHitList (unsigned long size)
virtual void	saveHitList (void)
virtual int	getMaxNumHits () const
virtual void	setMaxNumHits (int mnh)
virtual void	printHashStats (void)
virtual unsigned long	getTotalNumWords (void) const
void	setForward (void)
void	setReverse (void)
void	setQueryProtein (void)
void	setQueryTranslatedDNA (void)
bool	isForward (void) const
Protected Attributes
int	translatedWordLength_
HashTableComponent	hashFwd_
HashTableComponent	hashRev_
HashTableComponent *	pHash_
CodonList	codons_
SequenceEncoderCodon	codonEncoder_
MatchSequencePointer	pMatchSequence_
Private Member Functions
	HashTableTranslated (const HashTableTranslated &)
HashTableTranslated &	operator= (const HashTableTranslated &)

---

Detailed Description

Definition at line 141 of file HashTableTranslated.h.

---

Member Typedef Documentation

typedef void(HashTableTranslated::* ) HashTableTranslated::MatchSequencePointer(WordSequence &, HitList &)

Definition at line 147 of file HashTableTranslated.h.

---

Member Enumeration Documentation

anonymous enum

Enumerator:

eDNAWordSizeForHashing

Definition at line 149 of file HashTableTranslated.h.

{ eDNAWordSizeForHashing = gMaxBasesPerWord-1 };

---

Constructor & Destructor Documentation

HashTableTranslated::HashTableTranslated	(	ostream &	monitoringStream = cerr,
		string	name = "",
		Allocator< PositionPacked > &	hitListAllocator = HashTablePacked::defaultHitListAllocator,
		Allocator< PositionInHitList > &	arrayAllocator = HashTablePacked::defaultArrayAllocator
	)

Definition at line 248 of file HashTableTranslated.cpp.

References HashTableGeneric::bitsPerSymbol_, gResidueBits, gTranslated, HashTableGeneric::hitListFormat_, and HashTableGeneric::monitoringStream_.

    :
  hashFwd_( monitoringStream, name+(string)"_fwd", 
            hitListAllocator, arrayAllocator ),
  hashRev_( monitoringStream, name+(string)"_rev", 
            hitListAllocator, arrayAllocator ),
  pHash_(&hashFwd_),
  codonEncoder_(5),
  pMatchSequence_( &HashTableTranslated::matchSequenceProtein ),
  HashTableGeneric( monitoringStream, name, arrayAllocator ) 
{
  bitsPerSymbol_=gResidueBits;
  hitListFormat_ = gTranslated;
  monitoringStream_ << "constructing HashTableTranslated" << endl;
} // ~constructor

virtual HashTableTranslated::~HashTableTranslated

(

)

[inline, virtual]

Definition at line 169 of file HashTableTranslated.h.

{}

HashTableTranslated::HashTableTranslated

(

const HashTableTranslated &

)

[private]

---

Member Function Documentation

void HashTableTranslated::loadHashTable

(

SourceReaderIndex *

pSourceReader = NULL

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 540 of file HashTableTranslated.cpp.

References codonEncoder_, hashFwd_, hashRev_, HashTableGeneric::isInitialized_, loadFromFile(), HashTableGeneric::loadHashTable(), HashTableGeneric::loadSequenceNames(), HashTableGeneric::monitoringStream_, HashTableGeneric::name_, HashTableGeneric::pNameReader_, HashTableGeneric::pSequenceSizes_, pSourceReader, SequenceEncoder::setWordLength(), NameReader::size(), and HashTableGeneric::wordLength_.

Referenced by main().

{

  if (pSourceReader==NULL) 
  {
    pNameReader_ = new NameReaderLocal;
  } // ~if
  else
  {
    pNameReader_ = new NameReaderIndex(*pSourceReader);
  } // ~else

  // These have their own dummy NameReaders
  hashFwd_.loadHashTable();
  hashRev_.loadHashTable();
  loadSequenceNames();

  //  unsigned long numSeqs = sequenceNames_.size();
  unsigned long numSeqs = pNameReader_->size();

  assert(numSeqs!=0);

  monitoringStream_ << "Allocating memory for pSequenceSizes_: "
                    << numSeqs << " sequences, "
                    << numSeqs*sizeof(SequenceOffset)
                    << " bytes total ...\n";

  pSequenceSizes_ = new SequenceOffset [ numSeqs  ];
      
  if (!pSequenceSizes_) 
  {
    throw SSAHAException("Memory allocation failed!");
  } // ~if

  loadFromFile(name_+(string)".size", (char*)pSequenceSizes_, 
               numSeqs * sizeof( SequenceOffset ),
               monitoringStream_ );

  codonEncoder_.setWordLength( wordLength_ );

  isInitialized_=true;
}

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void HashTableTranslated::saveHashTable

(

void

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 584 of file HashTableTranslated.cpp.

References hashFwd_, hashRev_, and HashTableGeneric::saveHashTable().

Referenced by main().

{
  hashFwd_.saveHashTable();
  hashRev_.saveHashTable();
  HashTableGeneric::saveHashTable();
  //  saveSequenceNames();
}

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void HashTableTranslated::setupPointerArray

(

void

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 266 of file HashTableTranslated.cpp.

References HashTableGeneric::bitsPerSymbol_, gDNAData, gResidueBits, hashFwd_, hashRev_, HashTableGeneric::numDifferentWords_, HashTableGeneric::setupPointerArray(), HashTableGeneric::sourceData_, HashTableGeneric::stepLength_, and HashTableGeneric::wordLength_.

{

  hashFwd_.numDifferentWords_= 1 << (wordLength_*gResidueBits);
  hashFwd_.bitsPerSymbol_=gResidueBits;
  hashFwd_.sourceData_=gDNAData;
  hashFwd_.wordLength_=wordLength_;
  hashFwd_.stepLength_=stepLength_;
  hashFwd_.setupPointerArray();

  hashRev_.numDifferentWords_= 1 << (wordLength_*gResidueBits);
  hashRev_.bitsPerSymbol_=gResidueBits;
  hashRev_.sourceData_=gDNAData;
  hashRev_.wordLength_=wordLength_;
  hashRev_.stepLength_=stepLength_;
  hashRev_.setupPointerArray();
}

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int HashTableTranslated::countWordsAndGetNames	(	SequenceReader &	sequenceReader,
		SequenceAdapter *	seq
	)			[virtual]

Reimplemented from HashTableGeneric.

Definition at line 332 of file HashTableTranslated.cpp.

References SequenceEncoder::changeMode(), codonEncoder_, codonizeAndFlag(), codonizeAndFlagReverse(), codons_, HashTablePacked::countWords(), eDNAWordSizeForHashing, SequenceEncoder::encode(), SequenceReader::getLastSequenceName(), SequenceReader::getNextSequence(), gNumReadingFrames, hashFwd_, hashRev_, NameReaderLocal::lastName(), SequenceAdapter::link(), SequenceEncoder::linkSeq(), nv(), HashTableGeneric::pNameReader_, SequenceReader::rewind(), SequenceEncoder::setWordLength(), ttCodon, ttProtein, SequenceEncoder::unlinkSeq(), and HashTableGeneric::wordLength_.

{

    sequenceReader.rewind();

    //    CodonList codons; // make class member %%%%%
    //  SequenceEncoderCodon codonEncoder(5); // make class member %%%%%
    //    cout << "WordLength :" << wordLength_ << endl;
    NameReaderLocal* pReaderLocal = new NameReaderLocal;
    pNameReader_ = pReaderLocal;

    codonEncoder_.setWordLength(wordLength_);

    // Change encoding mode
    SequenceReaderModeFlagReplace mode('X');
    assert(ttCodon['X']==ttProtein['X']);
    assert(ttCodon['X']!=nv);
    codonEncoder_.changeMode( &mode );


    //    WordSequence thisSeq, revSeq, translatedSeq;
    WordSequence thisSeq, translatedSeq;
    seq->link( translatedSeq );
    int numSeqs(0);

    //    sequenceNames_.push_back(new string);


    while( sequenceReader.getNextSequence
           ( thisSeq, eDNAWordSizeForHashing ) != -1 ) 
    {
      numSeqs++;

      //      sequenceReader.getLastSequenceName( *(sequenceNames_.back()) );
      sequenceReader.getLastSequenceName( pReaderLocal->lastName() );
      //      sequenceNames_.push_back( new string );

      //    hashRev_.countWords(*seq);

      for ( int i(0) ; i < gNumReadingFrames ; i++ )
      {
        codons_.clear();
        codonizeAndFlag ( thisSeq, codons_, i );
        translatedSeq.clear();
        codonEncoder_.linkSeq( translatedSeq );
        codonEncoder_.encode( codons_ );
        codonEncoder_.unlinkSeq();
        hashFwd_.countWords(*seq);
      } // ~for i
      
      //      revSeq.clear();
      //    reverseComplement( thisSeq, revSeq, eDNAWordSizeForHashing);

      for ( int i(0) ; i < gNumReadingFrames ; i++ )
      {
        codons_.clear();
        codonizeAndFlagReverse ( thisSeq, codons_, i );
        translatedSeq.clear();
        codonEncoder_.linkSeq( translatedSeq );
        codonEncoder_.encode( codons_ );
        codonEncoder_.unlinkSeq();
        hashRev_.countWords(*seq);
      } // ~for i


    } // ~while

    //    pReaderLocal->pop_back();
    //   pNameReader_ = pReaderLocal;

    //    delete sequenceNames_.back();
    //   sequenceNames_.pop_back();
    //    wordSeqs.pop_back();

    return numSeqs;
} // ~HashTableTranslated::countWordsAndGetNames

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void HashTableTranslated::computePointerArray

(

void

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 285 of file HashTableTranslated.cpp.

References HashTableGeneric::computePointerArray(), hashFwd_, and hashRev_.

{
  hashFwd_.computePointerArray();
  hashRev_.computePointerArray();
}

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void HashTableTranslated::setupHitList

(

void

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 293 of file HashTableTranslated.cpp.

References hashFwd_, hashRev_, and HashTableGeneric::setupHitList().

{
  hashFwd_.setupHitList();
  hashRev_.setupHitList();
}

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void HashTableTranslated::hashAllWords	(	SequenceReader &	sequenceReader,
		SequenceAdapter *	seq,
		int	numSeqs
	)			[virtual]

Reimplemented from HashTableGeneric.

Definition at line 410 of file HashTableTranslated.cpp.

References SequenceEncoder::changeMode(), codonEncoder_, codonizeAndFlag(), codonizeAndFlagReverse(), codons_, eDNAWordSizeForHashing, SequenceEncoder::encode(), SequenceReader::getNextSequence(), gNumReadingFrames, hashFwd_, hashRev_, HashTablePacked::hashWords(), SequenceAdapter::link(), SequenceEncoder::linkSeq(), HashTableGeneric::pSequenceSizes_, SequenceReader::rewind(), and SequenceEncoder::unlinkSeq().

{

  //  cout << "HTT::hashAllWords" << endl;
  int numWords(0);
  sequenceReader.rewind();
  //  WordSequence thisSeq, revSeq, translatedSeq;
  WordSequence thisSeq, translatedSeq;
  seq->link( translatedSeq );

  // NB sequences are numbered 1...n not 0...n-1
  for ( unsigned int i(1); i <= numSeqs ; i++ )
  {
    //    cout << "hashing sequence " << i << endl;
    if( sequenceReader.getNextSequence( thisSeq, eDNAWordSizeForHashing) == -1 ) 
    {
      throw SSAHAException
        ("Sequence source data changed during hash table creation!");
    }

    // fill in the word count
    numWords = (int) thisSeq.size();
    pSequenceSizes_[i-1] = ( numWords > 0 ) 
      ? ( (numWords-1) * eDNAWordSizeForHashing ) + thisSeq.getNumBasesInLast()
      : 0;

    //    cout << "Fwd: " << printWord(thisSeq, eDNAWordSizeForHashing ) << endl;

    for ( int j(0) ; j < gNumReadingFrames ; j++ )
    {
      codons_.clear();
      codonizeAndFlag ( thisSeq, codons_, j );
      translatedSeq.clear();
      codonEncoder_.linkSeq( translatedSeq );
      codonEncoder_.encode( codons_ );
      codonEncoder_.unlinkSeq();

      //
      //            cout << "T" << j << ": ";
      //      for (WordSequence::iterator b(translatedSeq.begin());
      //   b!=translatedSeq.end();b++)
      //        cout << printResidue(*b, wordLength_ ) <<"-";
      //  cout << endl;


      hashFwd_.hashWords(*seq,99999);
    } // ~for
      
    //    revSeq.clear();
    //    reverseComplement( thisSeq, revSeq, eDNAWordSizeForHashing);
    
    //  cout << "Rev: " << printWord(thisSeq, eDNAWordSizeForHashing ) << endl;

    for ( int j(0) ; j < gNumReadingFrames ; j++ )
    {
      codons_.clear();
      codonizeAndFlagReverse ( thisSeq, codons_, j );
      translatedSeq.clear();
      codonEncoder_.linkSeq( translatedSeq );
      codonEncoder_.encode( codons_ );
      codonEncoder_.unlinkSeq();
      //           cout << "T" << j << ": ";
      //  for (WordSequence::iterator b(translatedSeq.begin());
      //    b!=translatedSeq.end();b++)
      //        cout << printResidue(*b, wordLength_ ) <<"-";
      //  cout << endl;

      hashRev_.hashWords(*seq,99999); // seqNum not needed for HTPacked::hash
    }

    // do the hashing
    //   seq->link(thisSeq);
    //   hashWords( *seq,i );
    //   cout << "hashallwords: " << wordLength_ << getWordLength() << endl;

  } // ~for thisSeq

  SequenceReaderModeIgnore mode;
  codonEncoder_.changeMode( &mode );


} // ~HashTableGeneric::hashAllWords 

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void HashTableTranslated::cleanupTempData

(

void

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 299 of file HashTableTranslated.cpp.

References HashTableGeneric::cleanupTempData(), hashFwd_, hashRev_, and HashTableGeneric::isInitialized_.

{
  hashFwd_.cleanupTempData();
  hashRev_.cleanupTempData();
  hashFwd_.isInitialized_=true;
  hashRev_.isInitialized_=true;
}

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void HashTableTranslated::hashWords	(	SequenceAdapter &	thisSeq,
		SequenceNumber	seqNum
	)			[virtual]

Implements HashTableGeneric.

Definition at line 309 of file HashTableTranslated.cpp.

References hashFwd_, hashRev_, and HashTablePacked::hashWords().

{
  assert(1==0);
  hashFwd_.hashWords( thisSeq, seqNum );
  hashRev_.hashWords( thisSeq, seqNum );
}

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void HashTableTranslated::countWords

(

SequenceAdapter &

thisSeq

)

[virtual]

Implements HashTableGeneric.

Definition at line 495 of file HashTableTranslated.cpp.

{
  assert(1==0);
  //  hashFwd_.countWords( thisSeq );
  //  hashRev_.countWords( thisSeq );
}

virtual void HashTableTranslated::matchSequence	(	WordSequence &	seq,
		HitList &	hitListFwd
	)			[inline, virtual]

Implements HashTableGeneric.

Definition at line 208 of file HashTableTranslated.h.

References pMatchSequence_.

Referenced by main().

  {
    (this->*pMatchSequence_)(seq, hitListFwd);
  }

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void HashTableTranslated::matchSequenceProtein	(	WordSequence &	seq,
		HitList &	hitListFwd
	)

Definition at line 608 of file HashTableTranslated.cpp.

References HashTablePacked::matchSequence(), pHash_, and HashTableComponent::setQueryFrame().

Referenced by main(), and setQueryProtein().

{
  //cout << "Trans::matchSequenceProtein, wordLength=" << wordLength_ << endl;
  //cout << printResidue( seq, wordLength_ ) << endl;
  pHash_->setQueryFrame(0);
  pHash_->matchSequence( seq, hitListFwd );
} // ~HashTableTranslated::matchSequenceProtein

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void HashTableTranslated::matchSequenceTranslatedDNA	(	WordSequence &	seq,
		HitList &	hitListFwd
	)

Definition at line 617 of file HashTableTranslated.cpp.

References codonEncoder_, codonize(), codons_, SequenceEncoder::encode(), gNumReadingFrames, SequenceEncoder::linkSeq(), HashTablePacked::matchSequence(), pHash_, HashTableComponent::setQueryFrame(), SequenceEncoder::setWordLength(), SequenceEncoder::unlinkSeq(), and HashTableGeneric::wordLength_.

Referenced by main(), and setQueryTranslatedDNA().

{
  //cout << "Trans::matchSequenceTranslatedDNA, wordLength=" << wordLength_ 
  //<< endl;
  codonEncoder_.setWordLength(wordLength_);
  WordSequence translatedSeq;
  for (int readingFrame(0); readingFrame < gNumReadingFrames; readingFrame++)
  {
    pHash_->setQueryFrame(readingFrame);
    codons_.clear();
    codonize ( seq, codons_, readingFrame );
    translatedSeq.clear();
    codonEncoder_.linkSeq( translatedSeq );
    codonEncoder_.encode( codons_ );
    codonEncoder_.unlinkSeq();
    //      cout << "T" << readingFrame << ": ";
    //  for (WordSequence::iterator b(translatedSeq.begin());
    //   b!=translatedSeq.end();b++)
    //       cout << printResidue(*b, wordLength_ ) <<"-";
    //   cout << endl;

    pHash_->matchSequence( translatedSeq, hitListFwd );
  } // ~for
} // ~HashTableTranslated::matchSequenceTranslatedDNA

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void HashTableTranslated::setNumRepeats

(

int

nr

)

[virtual]

Implements HashTableGeneric.

Definition at line 503 of file HashTableTranslated.cpp.

References hashFwd_, hashRev_, and HashTablePacked::setNumRepeats().

{
  hashFwd_.setNumRepeats( nr );
  hashRev_.setNumRepeats( nr );
}

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void HashTableTranslated::setSubstituteThreshold

(

int

ns

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 509 of file HashTableTranslated.cpp.

References hashFwd_, hashRev_, and HashTablePacked::setSubstituteThreshold().

{
  hashFwd_.setSubstituteThreshold( ns );
  hashRev_.setSubstituteThreshold( ns );
}

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char * HashTableTranslated::getHitListStart

(

void

)

const [virtual]

Implements HashTableGeneric.

Definition at line 515 of file HashTableTranslated.cpp.

{
  assert(1==0);
  return NULL;
}

int HashTableTranslated::getHitTypeSize

(

void

)

const [virtual]

Implements HashTableGeneric.

Definition at line 520 of file HashTableTranslated.cpp.

{
  assert(1==0);
  return NULL;
}

void HashTableTranslated::allocateHitList

(

unsigned long

size

)

[virtual]

Implements HashTableGeneric.

Definition at line 525 of file HashTableTranslated.cpp.

{
  assert(1==0);
}

void HashTableTranslated::loadHitList

(

unsigned long

size

)

[virtual]

Implements HashTableGeneric.

Definition at line 529 of file HashTableTranslated.cpp.

{
  assert(1==0);
}

void HashTableTranslated::saveHitList

(

void

)

[virtual]

Implements HashTableGeneric.

Definition at line 533 of file HashTableTranslated.cpp.

References HashTableGeneric::monitoringStream_.

{
  //  assert(1==0);
  monitoringStream_ << "No hit list to save for HashTableTranslated" << endl;
}

int HashTableTranslated::getMaxNumHits

(

)

const [virtual]

Reimplemented from HashTableGeneric.

Definition at line 316 of file HashTableTranslated.cpp.

References HashTableGeneric::getMaxNumHits(), hashFwd_, and hashRev_.

Referenced by main().

{ 
  assert( hashFwd_.getMaxNumHits() == hashRev_.getMaxNumHits() );
  return hashFwd_.getMaxNumHits();
} // ~getMaxNumHits() const 

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void HashTableTranslated::setMaxNumHits

(

int

mnh

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 321 of file HashTableTranslated.cpp.

References HashTableGeneric::getMaxNumHits(), hashFwd_, hashRev_, and HashTableGeneric::setMaxNumHits().

{ 
  hashFwd_.setMaxNumHits( mnh );
  hashRev_.setMaxNumHits( mnh );
  assert( hashFwd_.getMaxNumHits() == mnh );
  assert( hashFwd_.getMaxNumHits() == mnh );
} // ~setMaxNumHits( int mnh ) 

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void HashTableTranslated::printHashStats

(

void

)

[virtual]

Reimplemented from HashTableGeneric.

Definition at line 597 of file HashTableTranslated.cpp.

References hashFwd_, hashRev_, and HashTableGeneric::printHashStats().

{
  cout << "\n\n ** Hash stats output for forward subtable: ** \n\n";
  hashFwd_.printHashStats();
  cout << "\n\n ** Hash stats output for reverse subtable: ** \n\n";
  hashRev_.printHashStats();
} // ~HashTableTranslated::printHashStats( void )

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unsigned long HashTableTranslated::getTotalNumWords

(

void

)

const [virtual]

Reimplemented from HashTableGeneric.

Definition at line 592 of file HashTableTranslated.cpp.

References HashTableGeneric::getTotalNumWords(), hashFwd_, and hashRev_.

{
  return (hashFwd_.getTotalNumWords()+hashRev_.getTotalNumWords());
} // ~HashTableTranslated::getTotalNumWords( void ) const

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void HashTableTranslated::setForward

(

void

)

[inline]

Definition at line 240 of file HashTableTranslated.h.

References hashFwd_, and pHash_.

Referenced by main().

{ pHash_ = &hashFwd_; }

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void HashTableTranslated::setReverse

(

void

)

[inline]

Definition at line 241 of file HashTableTranslated.h.

References hashRev_, and pHash_.

Referenced by main().

{ pHash_ = &hashRev_; }

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void HashTableTranslated::setQueryProtein

(

void

)

[inline]

Definition at line 243 of file HashTableTranslated.h.

References matchSequenceProtein(), and pMatchSequence_.

Referenced by main().

  { 
    pMatchSequence_ = &HashTableTranslated::matchSequenceProtein;
  }

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void HashTableTranslated::setQueryTranslatedDNA

(

void

)

[inline]

Definition at line 247 of file HashTableTranslated.h.

References matchSequenceTranslatedDNA(), and pMatchSequence_.

Referenced by main().

  {
    pMatchSequence_ = &HashTableTranslated::matchSequenceTranslatedDNA;
  }

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bool HashTableTranslated::isForward

(

void

)

const [inline]

Definition at line 259 of file HashTableTranslated.h.

References hashFwd_, and pHash_.

Referenced by main(), MatchAdderProteinCodon::operator()(), and MatchAdderCodonCodon::operator()().

{ return (pHash_==&hashFwd_); }

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HashTableTranslated& HashTableTranslated::operator=

(

const HashTableTranslated &

)

[private]

---

Member Data Documentation

int HashTableTranslated::translatedWordLength_ [protected]

Definition at line 275 of file HashTableTranslated.h.

HashTableComponent HashTableTranslated::hashFwd_ [protected]

Definition at line 277 of file HashTableTranslated.h.

Referenced by cleanupTempData(), computePointerArray(), countWordsAndGetNames(), getMaxNumHits(), getTotalNumWords(), hashAllWords(), hashWords(), isForward(), loadHashTable(), HashTableTranslatedPeek::peekFwd(), printHashStats(), saveHashTable(), setForward(), setMaxNumHits(), setNumRepeats(), setSubstituteThreshold(), setupHitList(), and setupPointerArray().

HashTableComponent HashTableTranslated::hashRev_ [protected]

Definition at line 278 of file HashTableTranslated.h.

Referenced by cleanupTempData(), computePointerArray(), countWordsAndGetNames(), getMaxNumHits(), getTotalNumWords(), hashAllWords(), hashWords(), loadHashTable(), HashTableTranslatedPeek::peekRev(), printHashStats(), saveHashTable(), setMaxNumHits(), setNumRepeats(), setReverse(), setSubstituteThreshold(), setupHitList(), and setupPointerArray().

HashTableComponent* HashTableTranslated::pHash_ [protected]

Definition at line 279 of file HashTableTranslated.h.

Referenced by isForward(), matchSequenceProtein(), matchSequenceTranslatedDNA(), setForward(), and setReverse().

CodonList HashTableTranslated::codons_ [protected]

Definition at line 281 of file HashTableTranslated.h.

Referenced by countWordsAndGetNames(), hashAllWords(), matchSequenceTranslatedDNA(), and HashTablePackedProtein::matchSequenceTranslatedDNA().

SequenceEncoderCodon HashTableTranslated::codonEncoder_ [protected]

Definition at line 282 of file HashTableTranslated.h.

Referenced by countWordsAndGetNames(), hashAllWords(), loadHashTable(), matchSequenceTranslatedDNA(), and HashTablePackedProtein::matchSequenceTranslatedDNA().

MatchSequencePointer HashTableTranslated::pMatchSequence_ [protected]

Definition at line 284 of file HashTableTranslated.h.

Referenced by matchSequence(), setQueryProtein(), and setQueryTranslatedDNA().

---

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

• HashTable/HashTableTranslated.h
• HashTable/HashTableTranslated.cpp

---