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NCBI C++ ToolKit: src/algo/sequence/nuc_prop.cpp Source File

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44  table

.resize(NumberOfNmers(

n

));

47  for

(

int i

= 0;

i

< NumberOfNmers(

n

);

i

++) {

52

seqvec.GetSeqData(0,

len

, seq_string);

54

seq = seq_string.data();

57  int

nmerint = Nmer2Int(seq+

i

,

n

);

73  for

(

int i

= 0;

i

<

n

;

i

++) {

88  out

.resize(nmer_size);

89  for

(

int i

= nmer_size-1;

i

>= 0;

i

--) {

144  switch

(seqvec[

i

]) {

155  return

(

int

) ((gc_count * 100.0) /

len

+ 0.5);

this class defines functions for calculating various properties of nucleotide sequences

static void Int2Nmer(int nmer_int, int nmer_size, string &out)

Decode an integer representation of an n-mer.

static int Nmer2Int(const char *seq, int n)

Encode an n-mer as an integer.

static int NumberOfNmers(int n)

The number of distinct n-mers (4^n)

static int GetPercentGC(const CSeqVector &seqvec)

Calculate percent G+C+S.

static char Nybble2Nuc(int n)

static int Nuc2Nybble(char nuc)

std::ofstream out("events_result.xml")

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

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