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PssmMaker Class Reference

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#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

ConsensusMakerm_conMaker
 
bool m_useConsensus
 
bool m_addQuery
 
CRef< CSeq_entrym_masterSeqEntry
 
vector< char > m_trunctMaster
 
CCdCorem_cd
 
PssmMakerOptions m_config
 
short m_pseudoCount
 
CdPssmInputm_pssmInput
 
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 ( )
inline

Definition at line 149 of file cuPssmMaker.hpp.

References m_conMaker.

◆ getGuideAlignment()

const BlockModelPair & PssmMaker::getGuideAlignment ( )

◆ getPseudoCount()

short PssmMaker::getPseudoCount ( )
inline

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 ( )
private

◆ modifyQuery()

void PssmMaker::modifyQuery ( CRef< CSeq_entry query)
private

◆ 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
private

Definition at line 159 of file cuPssmMaker.hpp.

Referenced by make().

◆ m_cd

CCdCore* PssmMaker::m_cd
private

Definition at line 162 of file cuPssmMaker.hpp.

Referenced by make(), and modifyQuery().

◆ m_config

PssmMakerOptions PssmMaker::m_config
private

Definition at line 163 of file cuPssmMaker.hpp.

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

◆ m_conMaker

ConsensusMaker* PssmMaker::m_conMaker
private

◆ m_masterSeqEntry

CRef< CSeq_entry > PssmMaker::m_masterSeqEntry
private

Definition at line 160 of file cuPssmMaker.hpp.

Referenced by make(), and PssmMaker().

◆ m_pseudoCount

short PssmMaker::m_pseudoCount
private

Definition at line 164 of file cuPssmMaker.hpp.

Referenced by getPseudoCount(), and make().

◆ m_pssmInput

CdPssmInput* PssmMaker::m_pssmInput
private

◆ m_pssmMade

CRef<CPssmWithParameters> PssmMaker::m_pssmMade
private

Definition at line 168 of file cuPssmMaker.hpp.

Referenced by getGuideAlignment(), and make().

◆ m_trunctMaster

vector<char> PssmMaker::m_trunctMaster
private

Definition at line 161 of file cuPssmMaker.hpp.

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

◆ m_useConsensus

bool PssmMaker::m_useConsensus
private

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 modify_doxy.py rev. 669887