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CAntigenic Class Reference

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#include <algo/sequence/antigenic.hpp>

Public Types

typedef vector< CRef< objects::CSeq_loc > > TLocVec
 

Static Public Member Functions

static void PredictSites (const string &seq, TLocVec &results, unsigned int min_len=6)
 Predict antigenic determinants from protein sequence according to Kolaskar and Tongaonkar, 1990 (PMID 1702393). More...
 
static void PredictSites (const vector< char > &seq, TLocVec &results, unsigned int min_len=6)
 
static void PredictSites (const objects::CSeqVector &seq, TLocVec &results, unsigned int min_len=6)
 

Static Private Attributes

static const double sm_Pa_table [26]
 

Friends

template<class Seq >
void x_PredictAGSites (const Seq &seq, TLocVec &results, int min_len)
 

Detailed Description

Definition at line 44 of file antigenic.hpp.

Member Typedef Documentation

◆ TLocVec

typedef vector< CRef<objects::CSeq_loc> > CAntigenic::TLocVec

Definition at line 47 of file antigenic.hpp.

Member Function Documentation

◆ PredictSites() [1/3]

static void CAntigenic::PredictSites ( const objects::CSeqVector &  seq,
TLocVec results,
unsigned int  min_len = 6 
)
static

◆ PredictSites() [2/3]

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

Predict antigenic determinants from protein sequence according to Kolaskar and Tongaonkar, 1990 (PMID 1702393).

For std char containers, seq must be in ncbistdaa.

◆ PredictSites() [3/3]

static void CAntigenic::PredictSites ( const vector< char > &  seq,
TLocVec results,
unsigned int  min_len = 6 
)
static

Friends And Related Function Documentation

◆ x_PredictAGSites

template<class Seq >
void x_PredictAGSites ( const Seq &  seq,
CAntigenic::TLocVec results,
int  min_len 
)
friend

Definition at line 76 of file antigenic.cpp.

Member Data Documentation

◆ sm_Pa_table

const double CAntigenic::sm_Pa_table
staticprivate
Initial value:
=
{
0,
1.06383,
0.77624,
1.41226,
0.86646,
0.85083,
1.09132,
0.87413,
1.10505,
1.15173,
0.93026,
1.25039,
0.82567,
0.77624,
1.06383,
1.01542,
0.87254,
1.01219,
0.90884,
1.38428,
0.89290,
0.77624,
1.16148,
0.85083,
0,
0
}

Definition at line 66 of file antigenic.hpp.

Referenced by x_PredictAGSites().


The documentation for this class was generated from the following files:
Modified on Fri Jun 14 16:51:21 2024 by modify_doxy.py rev. 669887