NCBI C++ ToolKit
Classes | Macros | Functions | Variables
su_pssm.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistre.hpp>
#include <serial/serial.hpp>
#include <serial/objostrasn.hpp>
#include <algo/blast/api/pssm_input.hpp>
#include <algo/blast/api/pssm_engine.hpp>
#include <algo/blast/api/blast_aux.hpp>
#include <algo/blast/core/blast_encoding.h>
#include <objects/scoremat/scoremat__.hpp>
#include <algo/structure/struct_util/su_pssm.hpp>
#include <algo/structure/struct_util/su_block_multiple_alignment.hpp>
#include <algo/structure/struct_util/su_sequence_set.hpp>
#include "su_private.hpp"
+ Include dependency graph for su_pssm.cpp:

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Classes

class  SU_PSSMInput
 

Macros

#define PTHROW(stream)   NCBI_THROW(CException, eUnknown, stream)
 

Functions

 USING_SCOPE (objects)
 
 USING_SCOPE (blast)
 
static int Round (double Num)
 
int GetPSSMScoreOfCharWithAverageOfBZ (const BLAST_Matrix *matrix, unsigned int pssmIndex, char resChar)
 
static const string NCBIStdaaResidues ("-ABCDEFGHIKLMNPQRSTVWXYZU*OJ")
 
unsigned char LookupNCBIStdaaNumberFromCharacter (char r)
 
char LookupCharacterFromNCBIStdaaNumber (unsigned char n)
 
static void FillInAlignmentData (const BlockMultipleAlignment *bma, PSIMsa *data)
 
double GetStandardProbability (char ch)
 
static double CalculateInformationContent (const PSIMsa *data, bool ignoreMaster)
 
static BLAST_MatrixConvertPSSMToBLASTMatrix (const CPssmWithParameters &pssm)
 
BLAST_MatrixCreateBlastMatrix (const BlockMultipleAlignment *bma)
 

Variables

 USING_NCBI_SCOPE
 

Macro Definition Documentation

◆ PTHROW

#define PTHROW (   stream)    NCBI_THROW(CException, eUnknown, stream)

Definition at line 61 of file su_pssm.cpp.

Function Documentation

◆ CalculateInformationContent()

static double CalculateInformationContent ( const PSIMsa data,
bool  ignoreMaster 
)
static

◆ ConvertPSSMToBLASTMatrix()

static BLAST_Matrix* ConvertPSSMToBLASTMatrix ( const CPssmWithParameters pssm)
static

◆ CreateBlastMatrix()

BLAST_Matrix* CreateBlastMatrix ( const BlockMultipleAlignment bma)

◆ FillInAlignmentData()

static void FillInAlignmentData ( const BlockMultipleAlignment bma,
PSIMsa data 
)
static

◆ GetPSSMScoreOfCharWithAverageOfBZ()

int GetPSSMScoreOfCharWithAverageOfBZ ( const BLAST_Matrix matrix,
unsigned int  pssmIndex,
char  resChar 
)

◆ GetStandardProbability()

double GetStandardProbability ( char  ch)

◆ LookupCharacterFromNCBIStdaaNumber()

char LookupCharacterFromNCBIStdaaNumber ( unsigned char  n)

◆ LookupNCBIStdaaNumberFromCharacter()

unsigned char LookupNCBIStdaaNumberFromCharacter ( char  r)

◆ NCBIStdaaResidues()

static const string NCBIStdaaResidues ( "-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"  )
static

◆ Round()

static int Round ( double  Num)
inlinestatic

◆ USING_SCOPE() [1/2]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 52 of file su_pssm.cpp.

Modified on Sun Apr 14 05:26:23 2024 by modify_doxy.py rev. 669887