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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/kmercounts_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/cobalt/kmercounts.cpp Source File

objects::CScope& scope)

(index + kmer_len - 1 < sv.size() &&

< kmer_len) {

(sv[index +

] ==

) {

pos |=

(sv[index +

]) << (num_bits * (kmer_len -

- 1));

index = pos / chunk;

= pos - index * chunk;

num_bits)

counts =

[num_elements];

(std::bad_alloc) {

counts =

[num_elements];

(std::bad_alloc) {

);

objects::CScope& scope)

(kmer_len > 0 && alphabet_size > 0);

(!seq.IsWhole() && !seq.IsInt()) {

);

objects::CSeqVector sv = scope.GetBioseqHandle(*seq.GetId()).GetSeqVector();

num_elements;

seq_len = sv.size();

);

= 1;

(alphabet_size >

) {

kNumBits = num;

counts = tmp_counts.

();

num_elements = 1 << (kNumBits * kmer_len);

kMask = num_elements - (1 << kNumBits);

memset(counts, 0, num_elements *

(

));

kBitChunk =

(

) * 8;

vector<Uint4> used_entries(num_elements / kBitChunk + 1);

is_pos =

(sv, pos,

, kNumBits, kmer_len);

(pos, used_entries, kBitChunk);

(;

< seq_len && is_pos;

++) {

);

(sv[

] ==

) {

(

>= seq_len || !is_pos) {

(pos, used_entries, kBitChunk);

num_bit_chunks = num_elements / kBitChunk + 1;

(ind < num_elements / kBitChunk + 1) {

(ind < num_bit_chunks && used_entries[ind] == 0) {

(ind == num_bit_chunks) {

(

=0x80000000,j=0;used_entries[ind] != 0;

((used_entries[ind] &

) != 0) {

pos = ind * kBitChunk + j;

used_entries[ind] ^=

;

(pow((

)alphabet_size, (

)kmer_len)

(

=0;

< kmer_len;

++) {

base[

] = pow((

)alphabet_size, (

)

);

num_elements = (

)pow((

)alphabet_size, (double)kmer_len);

memset(counts, 0, num_elements *

(

));

kBitChunk =

(

) * 8;

vector<Uint4> used_entries(num_elements / kBitChunk + 1);

(

=0;

< seq_len - kmer_len + 1;

++) {

(sv[

+ kmer_len - 1] ==

) {

(

j=1;j < kmer_len;j++) {

(pos, used_entries, kBitChunk);

num_bit_chunks = num_elements / kBitChunk + 1;

(ind < num_elements / kBitChunk + 1) {

(ind < num_bit_chunks && used_entries[ind] == 0) {

(ind == num_bit_chunks) {

(

=0x80000000,j=0;used_entries[ind] != 0;

((used_entries[ind] &

) != 0) {

pos = ind * kBitChunk + j;

used_entries[ind] ^=

;

num_counts2 =

.GetNumCounts();

fewer_counts

= num_counts1 < num_counts2 ? num_counts1 : num_counts2;

1.0 - (double)num_common / (

)fewer_counts;

num_counts2 =

.GetNumCounts();

more_counts

= num_counts1 > num_counts2 ? num_counts1 : num_counts2;

1.0 - (double)num_common / (

)more_counts;

&& it1->position == it2->position) {

+= (unsigned)(it1->value < it2->value

? it1->value : it2->value);

&& it1->position < it2->position) {

&& it2->position < it1->position) {

= 1;

ostr << it->position <<

<< (

)it->value <<

;

objects::CScope& scope)

objects::CScope& scope)

(kmer_len > 0 && alphabet_size > 0);

(!seq.IsWhole() && !seq.IsInt()) {

);

objects::CSeqVector sv = scope.GetBioseqHandle(*seq.GetId()).GetSeqVector();

num_elements;

seq_len = sv.size();

);

kBitChunk =

(

) * 8;

(pow((

)alphabet_size, (

)kmer_len)

(

=0;

< kmer_len;

++) {

base[

] = pow((

)alphabet_size, (

)

);

num_elements = (

)pow((

)alphabet_size, (double)kmer_len);

(

j=0;j < kmer_len &&

< seq_len - kmer_len + 1;j++) {

(sv[

+ j] ==

) {

}

(

< seq_len - kmer_len + 1 && is_xaa);

(

>= seq_len - kmer_len + 1) {

(;

< seq_len - kmer_len + 1;

++) {

(sv[

+ kmer_len - 1] ==

) {

(

j=0;j < kmer_len &&

< seq_len - kmer_len + 1;

(sv[

+ j] ==

) {

}

(

< seq_len - kmer_len + 1 && is_xaa);

(

>= seq_len - kmer_len + 1) {

(

j=1;j < kmer_len;j++) {

num_counts2 =

.GetNumCounts();

fewer_counts

= num_counts1 < num_counts2 ? num_counts1 : num_counts2;

1.0 - (double)num_common / (

)fewer_counts;

num_counts2 =

.GetNumCounts();

more_counts

= num_counts1 > num_counts2 ? num_counts1 : num_counts2;

1.0 - (double)num_common / (

)more_counts;

(

=0;

<

;

++) {

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

ncbi::TMaskedQueryRegions mask

K-mer counts implemented as bit vectors.

static unsigned int GetKmerLength(void)

Get k-mer length.

static double FractionCommonKmersGlobalDist(const CBinaryKmerCounts &v1, const CBinaryKmerCounts &v2)

void Reset(const objects::CSeq_loc &seq, objects::CScope &scope)

Compute counts.

CBinaryKmerCounts(void)

Constructor.

unsigned int GetNumCounts(void) const

Get number of k-mers.

static unsigned int sm_AlphabetSize

static double FractionCommonKmersDist(const CBinaryKmerCounts &vect1, const CBinaryKmerCounts &vect2)

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 bool sm_UseCompressed

static Uint4 GetAALetter(Uint1 letter)

static unsigned int sm_KmerLength

static unsigned int CountCommonKmers(const CBinaryKmerCounts &v1, const CBinaryKmerCounts &v2)

Copmute number of common kmers between two count vectors.

Exception class for Kmer counts.

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.

CSparseKmerCounts(void)

Create empty counts vector.

static TCount * ReserveCountsMem(unsigned int num_bits)

vector< SVectorElement > m_Counts

vector< SVectorElement >::const_iterator TNonZeroCounts_CI

static double FractionCommonKmersGlobalDist(const CSparseKmerCounts &v1, const CSparseKmerCounts &v2)

static TCount * sm_Buffer

static void PreCount(void)

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

static CSafeStatic< vector< Uint1 > > sm_TransTable

static void PostCount(void)

Perform post-kmer counting tasks.

static const unsigned int kLengthBitsThreshold

TNonZeroCounts_CI BeginNonZero(void) const

Get non-zero counts iterator.

static unsigned int sm_KmerLength

static double FractionCommonKmersDist(const CSparseKmerCounts &vect1, const CSparseKmerCounts &vect2)

TNonZeroCounts_CI EndNonZero(void) const

Get non-zero counts iterator.

static Uint4 GetAALetter(Uint1 letter)

void Reset(const objects::CSeq_loc &seq, objects::CScope &scope)

Reset the counts vector.

unsigned int GetNumCounts(void) const

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

static bool sm_UseCompressed

static unsigned int CountCommonKmers(const CSparseKmerCounts &v1, const CSparseKmerCounts &v2, bool repetitions=true)

Copmute number of common kmers between two count vectors.

static bool sm_ForceSmallerMem

static bool InitPosBits(const objects::CSeqVector &sv, Uint4 &pos, unsigned int &index, Uint4 num_bits, Uint4 kmer_len)

Initializes element index as bit vector for first k letters, skipping Xaa.

CNcbiOstream & Print(CNcbiOstream &ostr) const

Print counts.

element_type * get(void) const

Get pointer.

void reset(element_type *p=0)

Reset will delete the old pointer, set content to the new value, and assume the ownership upon the ne...

#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

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

unsigned int

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

static void MarkUsed(Uint4 pos, vector< Uint4 > &entries, int chunk)

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

Defines NCBI C++ exception handling.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Element of the sparse vector.

static wxAcceleratorEntry entries[3]

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