HashTable/HashTablePacked.h File Reference

#include "HashTableGeneric.h"

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Classes
struct	PackedHitStore
class	RadixSorter
class	LessThanDiff
class	HashTablePacked
Typedefs
typedef unsigned int	PositionPacked
typedef unsigned int	SeqStartPos
typedef pair< PositionPacked, int >	HitPacked
Functions
void	generateSubstitutesDNA (Word w, vector< Word > &subs, int wordLength)
void	generateSubstitutesProtein (Word w, vector< Word > &subs, int wordLength)
Variables
static const HitPacked	zeroHit = HitPacked(0,0)
const Word	subVals []
const int	subStarts []

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Typedef Documentation

typedef pair<PositionPacked, int> HitPacked

Definition at line 47 of file HashTablePacked.h.

typedef unsigned int PositionPacked

Definition at line 44 of file HashTablePacked.h.

typedef unsigned int SeqStartPos

Definition at line 45 of file HashTablePacked.h.

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Function Documentation

void generateSubstitutesDNA	(	Word	w,
		vector< Word > &	subs,
		int	wordLength
	)

Definition at line 98 of file HashTablePacked.cpp.

References gBaseBits.

Referenced by main().

{
  Word mask(2);
  for (int i(0) ; i < wordLength ; i++, mask<<=gBaseBits)
  {
    subs.push_back(w^mask);
  } // ~for
} // ~generateSubstitutesDNA

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void generateSubstitutesProtein	(	Word	w,
		vector< Word > &	subs,
		int	wordLength
	)

Definition at line 110 of file HashTablePacked.cpp.

References gResidueBits, subStarts, and subVals.

Referenced by HashTableComponent::HashTableComponent(), HashTablePackedProtein::HashTablePackedProtein(), and main().

{
  Word mask((1<<gResidueBits)-1), thisCodon, thisWord;
  for (int i(0) ; i < wordLength ; i++, mask<<=gResidueBits)
  {
    thisCodon=((w&mask)>>(i*gResidueBits));
    thisWord= (w&(~mask));
    //    cout << ~mask << " " << printResidue( thisWord, wordLength )
    // << " " << printResidue( thisCodon, wordLength) << endl;
    for (int j(subStarts[thisCodon]); j != subStarts[thisCodon+1]; j++ )
    {
      subs.push_back( thisWord | (subVals[j]<<(i*gResidueBits)) );
      //  cout << "generating sub: " << printResidue(subs.back(),wordLength)
      //  << endl;
    } // ~for j
  } // ~for i
} // ~generateSubstitutesProtein

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Variable Documentation

const int subStarts[]

Initial value:

{
0,  
0,  
1,  
1,  
3,  
6,  
8,  
8,  
10, 
13, 
16, 
19, 
22, 
25, 
25, 
28, 
30, 
33, 
34, 
37, 
39, 
39, 
42
}

Definition at line 155 of file HashTablePacked.h.

Referenced by generateSubstitutesProtein(), and main().

const Word subVals[]

Initial value:

{
              
  16,         
              
              
  4,  12,     
  3,  9, 14,  
  19, 21,     
              
  12, 21,     
  10, 11, 18, 
  4,  14, 15, 
  8,  11, 18, 
  8,  10, 18, 
  3,  7,  16, 
              
  4,  9,  15, 
  9,  14,     
  1,  12, 17, 
  16,         
  8,  10, 11, 
  5,  21,     
  5,  7,  19, 
             
  99999
}

Definition at line 127 of file HashTablePacked.h.

Referenced by generateSubstitutesProtein(), and main().

const HitPacked zeroHit = HitPacked(0,0) [static]

Definition at line 56 of file HashTablePacked.h.

Referenced by RadixSorter::operator()().

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