HashTableComponent Class Reference

#include <HashTableTranslated.h>

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[legend]List of all members.

Public Member Functions
	HashTableComponent (ostream &monitoringStream, string name, Allocator< PositionPacked > &hitListAllocator=defaultHitListAllocator, Allocator< PositionInHitList > &arrayAllocator=defaultArrayAllocator)
virtual void	convertHits (PackedHitStore &hits, HitList &hitListFwd)
void	setQueryFrame (int qf)
Private Attributes
int	queryFrame_

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Detailed Description

Definition at line 55 of file HashTableTranslated.h.

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Constructor & Destructor Documentation

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

Definition at line 49 of file HashTableTranslated.cpp.

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

                    :
  queryFrame_(0),
  HashTablePacked( monitoringStream, name, 
                   hitListAllocator, arrayAllocator  ) 
{
  hitListFormat_ = g32BitPackedProtein;
  bitsPerSymbol_ = gResidueBits;
  pGenerateSubstitutes_ = &generateSubstitutesProtein;
  monitoringStream_ << "constructing HashTableComponent" << endl;
  pNameReader_ = new NameReader; // dummy, component contains no name info
} // ~constructor

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Member Function Documentation

void HashTableComponent::convertHits	(	PackedHitStore &	hits,
		HitList &	hitListFwd
	)			[virtual]

Reimplemented from HashTablePacked.

Definition at line 67 of file HashTableTranslated.cpp.

References HitListVector::addHit(), gNumReadingFrames, 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;

      adjustedSeqNum 
        = ub-seqStarts_.begin() - 1; // 0,1,2 ... etc.
      subjectFrame = adjustedSeqNum % gNumReadingFrames;
      adjustedSeqNum /= gNumReadingFrames;
      adjustedSeqNum++;


      //    cout 
      //        << "aHit: "
      //<< adjustedSeqNum << " " 
      //    << (gNumReadingFrames*stepLength_*(i->first - *j))+subjectFrame << " "
      //    << (gNumReadingFrames*i->second)+queryFrame_ << endl; 
        hitListFwd.addHit
          ( adjustedSeqNum,
            (gNumReadingFrames*stepLength_*(i->first - *j))+subjectFrame,
            (gNumReadingFrames*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

} // ~HashTableComponent::convertHits

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void HashTableComponent::setQueryFrame

(

int

qf

)

[inline]

Definition at line 68 of file HashTableTranslated.h.

References queryFrame_.

Referenced by HashTableTranslated::matchSequenceProtein(), and HashTableTranslated::matchSequenceTranslatedDNA().

{ queryFrame_ = qf; }

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Member Data Documentation

int HashTableComponent::queryFrame_ [private]

Definition at line 72 of file HashTableTranslated.h.

Referenced by HashTablePackedProtein::convertHits(), convertHits(), HashTablePackedProtein::matchSequenceTranslatedDNA(), and setQueryFrame().

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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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