HashTablePackedProtein Class Reference

#include <HashTableTranslated.h>

Inheritance diagram for HashTablePackedProtein:

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[legend]List of all members.

Public Types
typedef void(HashTablePackedProtein::*)	MatchSequencePointer (WordSequence &, HitList &)
Public Member Functions
	HashTablePackedProtein (ostream &monitoringStream, string name="", Allocator< PositionPacked > &hitListAllocator=defaultHitListAllocator, Allocator< PositionInHitList > &arrayAllocator=defaultArrayAllocator)
virtual void	convertHits (PackedHitStore &packedHits, HitList &hitListFwd)
virtual void	matchSequence (WordSequence &seq, HitList &hitListFwd)
void	matchSequenceProtein (WordSequence &seq, HitList &hitListFwd)
void	matchSequenceTranslatedDNA (WordSequence &seq, HitList &hitListFwd)
void	setQueryProtein (void)
void	setQueryTranslatedDNA (void)
Private Attributes
CodonList	codons_
SequenceEncoderCodon	codonEncoder_
int	queryFrame_
int	queryMult_
MatchSequencePointer	pMatchSequence_

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Detailed Description

Definition at line 85 of file HashTableTranslated.h.

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Member Typedef Documentation

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

Reimplemented from HashTablePacked.

Definition at line 89 of file HashTableTranslated.h.

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Constructor & Destructor Documentation

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

Definition at line 134 of file HashTableTranslated.cpp.

References HashTableGeneric::bitsPerSymbol_, g32BitPackedProtein, generateSubstitutesProtein(), gResidueBits, HashTableGeneric::hitListFormat_, HashTableGeneric::monitoringStream_, and HashTablePacked::pGenerateSubstitutes_.

   :
  queryFrame_(0),
  queryMult_(1),
  codonEncoder_(5),
  pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein ),
  HashTablePacked( monitoringStream, name, 
                     hitListAllocator, arrayAllocator  ) 
{
    hitListFormat_ = g32BitPackedProtein;
    bitsPerSymbol_ = gResidueBits;
    pGenerateSubstitutes_ = &generateSubstitutesProtein;
    monitoringStream_ << "constructing HashTablePackedProtein" << endl;
} // constructor

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Member Function Documentation

void HashTablePackedProtein::convertHits	(	PackedHitStore &	packedHits,
		HitList &	hitListFwd
	)			[virtual]

Reimplemented from HashTablePacked.

Definition at line 156 of file HashTableTranslated.cpp.

References HitListVector::addHit(), HashTableComponent::queryFrame_, HashTablePacked::seqStarts_, HashTablePacked::sorter_, and HashTableGeneric::stepLength_.

{


  //  sort(packedHits.begin(),packedHits.end());
  sorter_(packedHits);

  vector<HitPacked>::iterator i(packedHits.begin());
  vector<SeqStartPos>::iterator j(seqStarts_.begin());
  HitListVector::size_type sortStart;

  //SequenceNumber adjustedSeqNum;
  //int subjectFrame;

  //  hitListFwd.reserve(hitListFwd.size()+packedHits.size());

  // NB seqStarts_ must not be empty else call to back() segfaults

  while 
  (    (j!=static_cast<vector<SeqStartPos>::iterator>(&seqStarts_.back())) 
    && (i!=packedHits.end()) )
  {
    vector<SeqStartPos>::iterator ub(upper_bound(j,seqStarts_.end(),i->first));
    j=ub; j--;

    sortStart=hitListFwd.size();
    while ((i!=packedHits.end())&&(i->first<*ub))
    {
      //            cout << "Hit: " << i->first << " ... " 
      // << ub-seqStarts_.begin() << " " 
      // << stepLength_*(i->first - *j) << " "
      // << i->second      << endl;

            //    cout 
            //  << "aHit: "
            //  << ub-seqStarts_.begin() << " "
            //  << queryMult_*stepLength_*(i->first - *j) << " "
            //<< (queryMult_*i->second)+queryFrame_ << endl; 
        hitListFwd.addHit
          ( ub-seqStarts_.begin(), 
            (queryMult_*stepLength_*(i->first - *j)),
            (queryMult_*i->second)+queryFrame_); 
        //      hitListFwd.addHit( ub-seqStarts_.begin(), 
        //       stepLength_*(i->first - *j),
        //       i->second );
      i++;
      
    } // ~while i
    sort
    ( static_cast<HitList::iterator>(&hitListFwd[sortStart]),
      hitListFwd.end(),
      LessThanDiff() );
    j=ub;  
  } // ~while j


} // ~HashTablePackedProtein::convertHits

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

Reimplemented from HashTablePacked.

Definition at line 102 of file HashTableTranslated.h.

References pMatchSequence_.

Referenced by main().

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

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

Definition at line 215 of file HashTableTranslated.cpp.

References HashTablePacked::matchSequence().

Referenced by setQueryProtein().

{
  HashTablePacked::matchSequence( seq, hitListFwd );
} // ~HashTablePackedProtein::matchSequenceProtein

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

Definition at line 222 of file HashTableTranslated.cpp.

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

Referenced by setQueryTranslatedDNA().

{
  codonEncoder_.setWordLength( wordLength_ );

  WordSequence translatedSeq;
  for (queryFrame_ = 0; queryFrame_ < gNumReadingFrames; queryFrame_++)
  {
    codons_.clear();
    codonize ( seq, codons_, queryFrame_ );
    translatedSeq.clear();
    codonEncoder_.linkSeq( translatedSeq );
    codonEncoder_.encode( codons_ );
    codonEncoder_.unlinkSeq();
    HashTablePacked::matchSequence( translatedSeq, hitListFwd );
  } // ~for

} // ~HashTablePackedProtein::matchSequenceTranslatedDNA

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void HashTablePackedProtein::setQueryProtein

(

void

)

[inline]

Definition at line 110 of file HashTableTranslated.h.

References matchSequenceProtein(), pMatchSequence_, queryFrame_, and queryMult_.

Referenced by doSearch().

  { 
    pMatchSequence_ = &HashTablePackedProtein::matchSequenceProtein;
    queryMult_  = 1;
    queryFrame_ = 0;
  } 

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void HashTablePackedProtein::setQueryTranslatedDNA

(

void

)

[inline]

Definition at line 116 of file HashTableTranslated.h.

References gNumReadingFrames, matchSequenceTranslatedDNA(), pMatchSequence_, queryFrame_, and queryMult_.

  {
    pMatchSequence_ = &HashTablePackedProtein::matchSequenceTranslatedDNA;
    queryMult_  = gNumReadingFrames;
    queryFrame_ = 0;
  }

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Member Data Documentation

CodonList HashTablePackedProtein::codons_ [private]

Definition at line 124 of file HashTableTranslated.h.

SequenceEncoderCodon HashTablePackedProtein::codonEncoder_ [private]

Definition at line 125 of file HashTableTranslated.h.

int HashTablePackedProtein::queryFrame_ [private]

Definition at line 127 of file HashTableTranslated.h.

Referenced by setQueryProtein(), and setQueryTranslatedDNA().

int HashTablePackedProtein::queryMult_ [private]

Definition at line 128 of file HashTableTranslated.h.

Referenced by setQueryProtein(), and setQueryTranslatedDNA().

MatchSequencePointer HashTablePackedProtein::pMatchSequence_ [private]

Reimplemented from HashTablePacked.

Definition at line 130 of file HashTableTranslated.h.

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

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

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

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