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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/antigenic_8cpp_source.html below:

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

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84

vector<double> Pa(seq.size());

85  double

local_sum = 0, global_sum = 0;

87  for

(

int i

= 0;

i

< 7;

i

++) {

91

Pa[3] = local_sum / 7;

93  for

(

unsigned int i

= 4;

i

< seq.size() - 3;

i

++) {

97

Pa[

i

] = local_sum / 7;

100  double

global_mean = global_sum / seq.size();

101  double

thresh =

min

(global_mean, 1.0);

110  for

(

unsigned int i

= 3;

i

< seq.size() - 2;

i

++) {

111  if

(Pa[

i

] >= thresh) {

118  if

(

count

>= min_len) {

123

loc->SetInt().SetFrom(begin);

124

loc->SetInt().SetTo(end);

135  unsigned int

min_len)

143  unsigned int

min_len)

151  unsigned int

min_len)

153  string

seq_ncbistdaa;

156

vec.GetSeqData(0, vec.size(), seq_ncbistdaa);

void x_PredictAGSites(const Seq &seq, CAntigenic::TLocVec &results, int min_len)

vector< CRef< objects::CSeq_loc > > TLocVec

static void PredictSites(const string &seq, TLocVec &results, unsigned int min_len=6)

Predict antigenic determinants from protein sequence according to Kolaskar and Tongaonkar,...

friend void x_PredictAGSites(const Seq &seq, TLocVec &results, int min_len)

static const double sm_Pa_table[26]

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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