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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/kmercounts_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/cobalt/kmercounts.hpp Source File

objects::CScope& scope);

Reset(

objects::CSeq_loc& seq, objects::CScope& scope);

{sm_KmerLength =

; sm_ForceSmallerMem =

;}

{sm_AlphabetSize =

; sm_ForceSmallerMem =

;}

repetitions =

);

PreCount(

);

PostCount(

);

TCount* ReserveCountsMem(

num_bits);

(!sm_UseCompressed || letter < sm_TransTable->

());

(

)(sm_UseCompressed ? (sm_TransTable.Get())[(

)

] :

);

InitPosBits(

objects::CSeqVector& sv,

& pos,

& index,

num_bits,

kLengthBitsThreshold = 32;

objects::CScope& scope);

Reset(

objects::CSeq_loc& seq, objects::CScope& scope);

{sm_KmerLength =

;}

{sm_AlphabetSize =

;}

(!sm_UseCompressed || letter < sm_TransTable->

());

(

)(sm_UseCompressed ? (sm_TransTable.Get())[(

)

] :

);

v = v - ((v >> 1) & 0x55555555);

v = (v & 0x33333333) + ((v >> 2) & 0x33333333);

v = ((v + (v >> 4)) & 0xF0F0F0F);

<

TKmerCounts>

(

kmer_len,

alphabet_size)

TKmerCounts::SetKmerLength(kmer_len);

TKmerCounts::SetAlphabetSize(alphabet_size);

TKmerCounts::SetTransTable().clear();

TKmerCounts::SetUseCompressed(

);

vector<Uint1>& trans_table,

alphabet_len)

* kCompAlphabets[] = {

,

* trans_string = kCompAlphabets[alph_index

compressed_letter = 1;

trans_table.resize(alphabet_len + 1, 0);

(

= 0;

< strlen(trans_string);

++) {

(

(trans_string[

])) {

(aa_letter < trans_table.size());

trans_table[aa_letter] = compressed_letter;

TKmerCounts::SetKmerLength(kmer_len);

TKmerCounts::SetTransTable(),

TKmerCounts::SetUseCompressed(

);

TKmerCounts::SetTransTable(),

TKmerCounts::SetUseCompressed(

);

TKmerCounts::SetTransTable().clear();

TKmerCounts::SetUseCompressed(

);

objects::CScope& scope,

vector<TKmerCounts>& counts)

);

TKmerCounts::PreCount();

counts.push_back(TKmerCounts(**it, scope));

TKmerCounts::PostCount();

(*fsim)(

TKmerCounts&,

TKmerCounts&),

(counts.empty()) {

);

dmat.

(counts.size(), counts.size(), 0.0);

(

=0;

< (

)counts.size() - 1;

++) {

(

j=

+1;j < (

)counts.size();j++) {

dmat(

, j) = fsim(counts[

], counts[j]);

dmat(j,

) = dmat(

, j);

(*fsim)(

TKmerCounts&,

TKmerCounts&,

,

),

vector<double>& normalizers);

(dist_method) {

TKmerCounts::FractionCommonKmersGlobalDist,

);

vector<TKmerCounts>& counts,

unique_ptr<TDistMatrix> dmat(

(counts.size(),

(counts.size() < 2) {

);

(

=0;

< (

)counts.size()-1;

++) {

(

j=

+1;j < (

)counts.size();j++) {

dist = TKmerCounts::FractionCommonKmersDist(counts[

],

dist = TKmerCounts::FractionCommonKmersGlobalDist(counts[

],

(dist <= max_dist) {

Definitions used by all COBALT aligner components.

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

K-mer counts implemented as bit vectors.

static void SetUseCompressed(bool use_comp)

Set default option for using compressed alphabet.

static unsigned int GetKmerLength(void)

Get k-mer length.

unsigned int GetSeqLength(void) const

Get sequence length.

static void PostCount(void)

Perform post-kmer counting tasks.

static unsigned int GetAlphabetSize(void)

Get alphabet size.

static void SetKmerLength(unsigned len)

Set default k-mer length.

CBinaryKmerCounts(void)

Constructor.

unsigned int GetNumCounts(void) const

Get number of k-mers.

static unsigned int sm_AlphabetSize

static void SetAlphabetSize(unsigned size)

Set Default alphabet size.

static Uint4 x_Popcount(Uint4 v)

Get number of set bits (adapted from http://graphics.stanford.edu/~seander/bithacks....

static CSafeStatic< vector< Uint1 > > sm_TransTable

static void PreCount(void)

Perform preparations before k-mer counting common to all sequences.

static bool sm_UseCompressed

static vector< Uint1 > & SetTransTable(void)

Set default compressed alphabet letter translation table.

static Uint4 GetAALetter(Uint1 letter)

static unsigned int sm_KmerLength

Exception class for Kmer counts.

NCBI_EXCEPTION_DEFAULT(CKmerCountsException, CException)

Set of edges with weights between nodes represented by zero-based positive integers.

void AddLink(int first, int second, double weight)

Add link.

void Resize(size_t i, size_t j, T val=T())

resize this matrix, filling the empty cells with a known value

Kmer counts for alignment free sequence similarity computation implemented as a sparse vector.

static unsigned int sm_AlphabetSize

static unsigned int GetKmerLength(void)

Get default kmer length.

static void SetUseCompressed(bool use_comp)

Set default option for using compressed alphabet.

CSparseKmerCounts(void)

Create empty counts vector.

vector< SVectorElement > m_Counts

vector< SVectorElement >::const_iterator TNonZeroCounts_CI

static TCount * sm_Buffer

static CSafeStatic< vector< Uint1 > > sm_TransTable

static unsigned int GetAlphabetSize(void)

Get default alphabet size.

TNonZeroCounts_CI BeginNonZero(void) const

Get non-zero counts iterator.

static unsigned int sm_KmerLength

TNonZeroCounts_CI EndNonZero(void) const

Get non-zero counts iterator.

static Uint4 GetAALetter(Uint1 letter)

static void SetAlphabetSize(unsigned size)

Set Default alphabet size.

unsigned int GetNumCounts(void) const

Get number of all k-mers found in the sequence.

static bool sm_UseCompressed

static bool sm_ForceSmallerMem

unsigned int GetSeqLength(void) const

Get sequence length.

static void SetKmerLength(unsigned len)

Set default k-mer length.

static vector< Uint1 > & SetTransTable(void)

Set default compressed alphabet letter translation table.

Interface for computing and manipulating k-mer counts vectors that allows for different implementatio...

static CRef< CLinks > ComputeDistLinks(const vector< TKmerCounts > &counts, EDistMeasures dist_method, double max_dist)

Compute distances between k-mer counts as graph where nodes are sequences and edges represent distanc...

static void ComputeDistMatrix(const vector< TKmerCounts > &counts, double(*fsim)(const TKmerCounts &, const TKmerCounts &), TDistMatrix &dmat)

Compute matrix of distances between given counts vectors.

static void SetParams(unsigned kmer_len, ECompressedAlphabet alph)

Set default counts vector parameters for use with compressed alphabet.

static unique_ptr< TDistMatrix > ComputeDistMatrix(const vector< TKmerCounts > &counts, EDistMeasures dist_method)

Compute distance matrix for given counts vectors and distance measure and avoid copying.

static void ComputeDistMatrix(const vector< TKmerCounts > &counts, TDistMatrix &dmat, double(*fsim)(const TKmerCounts &, const TKmerCounts &, double, double), const vector< double > &normalizers)

Compute matrix of distances between given list of counts vectors using distance function with additio...

static void BuildCompressedTranslation(ECompressedAlphabet alph_index, vector< Uint1 > &trans_table, unsigned alphabet_len)

Creates translation table for compressed alphabets.

CNcbiMatrix< double > TDistMatrix

@ eFractionCommonKmersLocal

@ eFractionCommonKmersGlobal

static void ComputeCounts(const vector< CRef< objects::CSeq_loc > > &seqs, objects::CScope &scope, vector< TKmerCounts > &counts)

Create k-mer counts vectors for given sequences.

static void ComputeDistMatrix(const vector< TKmerCounts > &counts, EDistMeasures dist_method, TDistMatrix &dmat)

Compute distance matrix for given counts vectors and distance measure.

static void SetParams(unsigned kmer_len, unsigned alphabet_size)

Set default counts vector parameters.

void Print(const CCompactSAMApplication::AlignInfo &ai)

static ulg compressed_len

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

#define NCBI_COBALT_EXPORT

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

Static variables safety - create on demand, destroy on application termination.

Element of the sparse vector.

SVectorElement(Uint4 pos, TCount val)

Create vector element.

Uint4 position

position of non-zero element

SVectorElement(void)

Default constructor.

TCount value

value of non-zero element

static Uint4 letter(char c)

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