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PSSMWrapper Class Reference

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#include "cn3d_pssm.hpp"
(Private to src/app/cn3d.)

+ Collaboration diagram for PSSMWrapper:

Public Member Functions

 PSSMWrapper (const BlockMultipleAlignment *bma)
 
int GetPSSMScore (unsigned char ncbistdaa, unsigned int realMasterIndex) const
 
void OutputPSSM (ncbi::CNcbiOstream &os, const std::string &title) const
 
const ncbi::objects::CPssmWithParameters & GetPSSM (void) const
 
int MapConsensusToMaster (unsigned int consensusIndex) const
 

Private Types

typedef std::vector< intColumn
 

Private Member Functions

void UnpackMatrix (ncbi::cd_utils::PssmMaker &pm)
 

Private Attributes

const BlockMultipleAlignmentmultiple
 
ncbi::CRef< ncbi::objects::CPssmWithParameters > pssm
 
std::vector< ColumnscaledMatrix
 
int scalingFactor
 
std::vector< intmaster2consensus
 
std::vector< intconsensus2master
 

Detailed Description

Definition at line 55 of file cn3d_pssm.hpp.

Member Typedef Documentation

◆ Column

typedef std::vector< int > PSSMWrapper::Column
private

Definition at line 61 of file cn3d_pssm.hpp.

Constructor & Destructor Documentation

◆ PSSMWrapper()

PSSMWrapper::PSSMWrapper ( const BlockMultipleAlignment bma)

Member Function Documentation

◆ GetPSSM()

const ncbi::objects::CPssmWithParameters& PSSMWrapper::GetPSSM ( void  ) const
inline

Definition at line 73 of file cn3d_pssm.hpp.

References pssm.

◆ GetPSSMScore()

int PSSMWrapper::GetPSSMScore ( unsigned char  ncbistdaa,
unsigned int  realMasterIndex 
) const

◆ MapConsensusToMaster()

int PSSMWrapper::MapConsensusToMaster ( unsigned int  consensusIndex) const
inline

Definition at line 74 of file cn3d_pssm.hpp.

References consensus2master.

◆ OutputPSSM()

void PSSMWrapper::OutputPSSM ( ncbi::CNcbiOstream os,
const std::string title 
) const

Definition at line 265 of file cn3d_pssm.cpp.

References copy(), ERRORMSG, i, pssm, and CSeqdesc_Base::SetTitle().

◆ UnpackMatrix()

void PSSMWrapper::UnpackMatrix ( ncbi::cd_utils::PssmMaker &  pm)
private

Member Data Documentation

◆ consensus2master

std::vector< int > PSSMWrapper::consensus2master
private

Definition at line 64 of file cn3d_pssm.hpp.

Referenced by MapConsensusToMaster(), and UnpackMatrix().

◆ master2consensus

std::vector< int > PSSMWrapper::master2consensus
private

Definition at line 64 of file cn3d_pssm.hpp.

Referenced by GetPSSMScore(), and UnpackMatrix().

◆ multiple

const BlockMultipleAlignment* PSSMWrapper::multiple
private

Definition at line 57 of file cn3d_pssm.hpp.

Referenced by GetPSSMScore(), PSSMWrapper(), and UnpackMatrix().

◆ pssm

ncbi::CRef< ncbi::objects::CPssmWithParameters > PSSMWrapper::pssm
private

Definition at line 58 of file cn3d_pssm.hpp.

Referenced by GetPSSM(), OutputPSSM(), PSSMWrapper(), and UnpackMatrix().

◆ scaledMatrix

std::vector< Column > PSSMWrapper::scaledMatrix
private

Definition at line 62 of file cn3d_pssm.hpp.

Referenced by GetPSSMScore(), and UnpackMatrix().

◆ scalingFactor

int PSSMWrapper::scalingFactor
private

Definition at line 63 of file cn3d_pssm.hpp.

Referenced by GetPSSMScore(), and UnpackMatrix().


The documentation for this class was generated from the following files:
Modified on Sun Jun 16 04:38:17 2024 by modify_doxy.py rev. 669887