54 unsigned int CSparseKmerCounts::sm_KmerLength = 4;
55 unsigned int CSparseKmerCounts::sm_AlphabetSize = kAlphabetSize;
56 vector<Uint1> CSparseKmerCounts::sm_TransTable;
57 bool CSparseKmerCounts::sm_UseCompressed = false;
58 CSparseKmerCounts::TCount* CSparseKmerCounts::sm_Buffer = NULL;
59 bool CSparseKmerCounts::sm_ForceSmallerMem = false;
69 CSparseKmerCounts::CSparseKmerCounts(const objects::CSeq_loc& seq,  in CSparseKmerCounts()  function in CSparseKmerCounts
82 bool CSparseKmerCounts::InitPosBits(const objects::CSeqVector& sv, Uint4& pos,  in InitPosBits()
121 CSparseKmerCounts::TCount* CSparseKmerCounts::ReserveCountsMem(  in ReserveCountsMem()
157 void CSparseKmerCounts::Reset(const objects::CSeq_loc& seq,  in Reset()
366 double CSparseKmerCounts::FractionCommonKmersDist(  in FractionCommonKmersDist()
367                                                   const CSparseKmerCounts& v1,  in FractionCommonKmersDist()
368                                                   const CSparseKmerCounts& v2)  in FractionCommonKmersDist()
386 double CSparseKmerCounts::FractionCommonKmersGlobalDist(  in FractionCommonKmersGlobalDist()
387                                                   const CSparseKmerCounts& v1,  in FractionCommonKmersGlobalDist()
388                                                   const CSparseKmerCounts& v2)  in FractionCommonKmersGlobalDist()
406 unsigned int CSparseKmerCounts::CountCommonKmers(  in CountCommonKmers()
407                                               const CSparseKmerCounts& vect1,   in CountCommonKmers()
408                                               const CSparseKmerCounts& vect2,  in CountCommonKmers()
454 void CSparseKmerCounts::PreCount(void)  in PreCount()
468 void CSparseKmerCounts::PostCount(void)  in PostCount()
478 CNcbiOstream& CSparseKmerCounts::Print(CNcbiOstream& ostr) const  in Print()
480     for (CSparseKmerCounts::TNonZeroCounts_CI it=BeginNonZero();  in Print()