HashTablePackedCustom Class Reference

Inheritance diagram for HashTablePackedCustom:

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[legend]List of all members.

Public Member Functions
	HashTablePackedCustom (ostream &monitoringStream=cerr, string name="")
void	convertHits (void)

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Detailed Description

Definition at line 72 of file SSAHAWrapper.cpp.

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Constructor & Destructor Documentation

HashTablePackedCustom::HashTablePackedCustom	(	ostream &	monitoringStream = cerr,
		string	name = ""
	)			[inline]

Definition at line 76 of file SSAHAWrapper.cpp.

Referenced by loadTable().

                                                                          :
    HashTablePackedProtein( monitoringStream, name ) 
    {}

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Member Function Documentation

void HashTablePackedCustom::convertHits

(

void

)

Definition at line 88 of file SSAHAWrapper.cpp.

References hitBuffer, hits, HashTablePacked::seqStarts_, and HashTableGeneric::stepLength_.

Referenced by doSearch().

{

  //  sort(hitBuffer.begin(),hitBuffer.end());

  vector<HitPacked>::iterator i(hitBuffer.begin());
  vector<SeqStartPos>::iterator j(seqStarts_.begin());
  //  hitListFwd.reserve(hitListFwd.size()+hitBuffer.size());
  hits.reserve( hits.size() + hitBuffer.size());

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

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

    while ((i!=hitBuffer.end())&&(i->first<*ub))
    {
      //      cout << i->first << " ... " 
      //   << ub-seqStarts_.begin() << " " 
      //   << stepLength_*(i->first - *j) 
      //   << endl;
      //      hitListFwd.addHit( ub-seqStarts_.begin(), 
      //                    stepLength_*(i->first - *j),
      //                    i->second );
      hits.push_back();
      hits.back().seqNum= ub-seqStarts_.begin();
      hits.back().seqPos= stepLength_*(i->first - *j);
      //      hitListFwd.addHit( 
      //                    
      //                    i->second );
      
      i++;
      
    } // ~while
    j=ub;  
  } // ~while

} // ~HashTablePackedCustom::convertHits( void )

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

• EnsemblServer/SSAHAWrapper.cpp

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