NCBI C++ ToolKit
Public Member Functions | Private Member Functions | Private Attributes | List of all members
PssmMaker Class Reference

Search Toolkit Book for PssmMaker

#include <algo/structure/cd_utils/cuPssmMaker.hpp>

+ Collaboration diagram for PssmMaker:

Public Member Functions

 PssmMaker (CCdCore *cd, bool useConsensus=true, bool addQueryToPssm=true)
 ~PssmMaker ()
void setOptions (const PssmMakerOptions &option)
CRef< CPssmWithParametersmake ()
bool getTrunctMaster (CRef< CSeq_entry > &seqEntry)
const BlockModelPairgetGuideAlignment ()
const stringgetConsensus ()
short getPseudoCount ()
ConsensusMakergetConsensusMaker ()
void printAlignment (string &fileName)
void printAlignmentByColumn (string &fileName)
void getPssmColumnResidues (map< unsigned int, string > &columnMap)

Private Member Functions

void modifyQuery (CRef< CSeq_entry > query)
CRef< CPssmWithParametersmakeDefaultPssm ()

Private Attributes

bool m_useConsensus
bool m_addQuery
CRef< CSeq_entrym_masterSeqEntry
vector< char > m_trunctMaster
PssmMakerOptions m_config
short m_pseudoCount
CRef< CPssmWithParametersm_pssmMade

Detailed Description

Definition at line 135 of file cuPssmMaker.hpp.

Constructor & Destructor Documentation

◆ PssmMaker()

PssmMaker::PssmMaker ( CCdCore cd,
bool  useConsensus = true,
bool  addQueryToPssm = true 

◆ ~PssmMaker()

PssmMaker::~PssmMaker ( )

Definition at line 346 of file cuPssmMaker.cpp.

References m_conMaker, and m_pssmInput.

Member Function Documentation

◆ getConsensus()

const string & PssmMaker::getConsensus ( )

Definition at line 550 of file cuPssmMaker.cpp.

References ConsensusMaker::getConsensus(), and m_conMaker.

Referenced by CDUpdater::blast().

◆ getConsensusMaker()

ConsensusMaker& PssmMaker::getConsensusMaker ( )

Definition at line 149 of file cuPssmMaker.hpp.

References m_conMaker.

◆ getGuideAlignment()

const BlockModelPair & PssmMaker::getGuideAlignment ( )

◆ getPseudoCount()

short PssmMaker::getPseudoCount ( )

Definition at line 148 of file cuPssmMaker.hpp.

References m_pseudoCount.

Referenced by CDUpdater::blast().

◆ getPssmColumnResidues()

void PssmMaker::getPssmColumnResidues ( map< unsigned int, string > &  columnMap)

◆ getTrunctMaster()

bool PssmMaker::getTrunctMaster ( CRef< CSeq_entry > &  seqEntry)

◆ make()

CRef< CPssmWithParameters > PssmMaker::make ( )

◆ makeDefaultPssm()

CRef< CPssmWithParameters > PssmMaker::makeDefaultPssm ( )

◆ modifyQuery()

void PssmMaker::modifyQuery ( CRef< CSeq_entry query)

◆ printAlignment()

void PssmMaker::printAlignment ( string fileName)

◆ printAlignmentByColumn()

void PssmMaker::printAlignmentByColumn ( string fileName)

◆ setOptions()

void PssmMaker::setOptions ( const PssmMakerOptions option)

Definition at line 341 of file cuPssmMaker.cpp.

References m_config, and option.

Referenced by CDUpdater::blast().

Member Data Documentation

◆ m_addQuery

bool PssmMaker::m_addQuery

Definition at line 159 of file cuPssmMaker.hpp.

Referenced by make().

◆ m_cd

CCdCore* PssmMaker::m_cd

Definition at line 162 of file cuPssmMaker.hpp.

Referenced by make(), and modifyQuery().

◆ m_config

PssmMakerOptions PssmMaker::m_config

Definition at line 163 of file cuPssmMaker.hpp.

Referenced by make(), makeDefaultPssm(), modifyQuery(), and setOptions().

◆ m_conMaker

ConsensusMaker* PssmMaker::m_conMaker

◆ m_masterSeqEntry

CRef< CSeq_entry > PssmMaker::m_masterSeqEntry

Definition at line 160 of file cuPssmMaker.hpp.

Referenced by make(), and PssmMaker().

◆ m_pseudoCount

short PssmMaker::m_pseudoCount

Definition at line 164 of file cuPssmMaker.hpp.

Referenced by getPseudoCount(), and make().

◆ m_pssmInput

CdPssmInput* PssmMaker::m_pssmInput

◆ m_pssmMade

CRef<CPssmWithParameters> PssmMaker::m_pssmMade

Definition at line 168 of file cuPssmMaker.hpp.

Referenced by getGuideAlignment(), and make().

◆ m_trunctMaster

vector<char> PssmMaker::m_trunctMaster

Definition at line 161 of file cuPssmMaker.hpp.

Referenced by getTrunctMaster(), make(), and makeDefaultPssm().

◆ m_useConsensus

bool PssmMaker::m_useConsensus

Definition at line 158 of file cuPssmMaker.hpp.

Referenced by getTrunctMaster(), make(), makeDefaultPssm(), and PssmMaker().

The documentation for this class was generated from the following files:
Modified on Sat May 25 14:16:51 2024 by rev. 669887