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ColumnResidueProfile Class Reference

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

+ Collaboration diagram for ColumnResidueProfile:

Public Types

typedef pair< int, boolRowStatusPair
typedef multimap< char, RowStatusPairResidueRowsMap

Public Member Functions

 ColumnResidueProfile ()
 ~ColumnResidueProfile ()
void addOccurence (char residue, int row, bool aligned)
double calculateColumnWeight (char residue, bool countGap, int numRows) const
double sumUpColumnWeightsByRow (vector< double > &rowWeights, bool countGap, int numRows) const
double reweightColumnByRowWeights (const vector< double > &rowWeights, char &heaviestResidue) const
int getSumCount () const
char getMostFrequentResidue (int &count) const
void getResiduesByRow (vector< char > &residues, bool byNcbiStd=true) const
unsigned char getResidueByRow (int row)
bool isAligned (char residue, int row) const
bool isAligned (int row)
bool isAllRowsAligned () const
void setIndexByConsensus (int col)
int getIndexByConsensus () const
int getResidueTypeCount () const
double calcInformationContent ()

Static Public Member Functions

static unsigned char getNcbiStdCode (char eaa)
static char getEaaCode (char stdCode)

Static Public Attributes

static const string m_residues = "-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"

Private Member Functions

ResidueRowsMap::iteratorfindRow (int row)
double getBackgroundResFreq (char res)

Static Private Member Functions

static void useDefaultBackgroundResFreq ()

Private Attributes

bool m_masterIn
ResidueRowsMap m_residueRowsMap
vector< ResidueRowsMap::iterator * > m_residuesByRow
int m_residueTypeCount
int m_indexByConsensus

Static Private Attributes

static map< char, double > m_backgroundResFreq

Detailed Description

Definition at line 45 of file cuResidueProfile.hpp.

Member Typedef Documentation

◆ ResidueRowsMap

Definition at line 73 of file cuResidueProfile.hpp.

◆ RowStatusPair

Definition at line 72 of file cuResidueProfile.hpp.

Constructor & Destructor Documentation

◆ ColumnResidueProfile()

ColumnResidueProfile::ColumnResidueProfile ( )

Definition at line 45 of file cuResidueProfile.cpp.

◆ ~ColumnResidueProfile()

ColumnResidueProfile::~ColumnResidueProfile ( )

Definition at line 51 of file cuResidueProfile.cpp.

References i, and m_residuesByRow.

Member Function Documentation

◆ addOccurence()

void ColumnResidueProfile::addOccurence ( char  residue,
int  row,
bool  aligned 

◆ calcInformationContent()

double ColumnResidueProfile::calcInformationContent ( )

◆ calculateColumnWeight()

double ColumnResidueProfile::calculateColumnWeight ( char  residue,
bool  countGap,
int  numRows 
) const

Definition at line 120 of file cuResidueProfile.cpp.

References getSumCount(), m_residueRowsMap, and m_residueTypeCount.

Referenced by sumUpColumnWeightsByRow().

◆ findRow()

ResidueRowsMap::iterator* ColumnResidueProfile::findRow ( int  row)

Definition at line 79 of file cuResidueProfile.hpp.

References row.

Referenced by getResidueByRow(), and isAligned().

◆ getBackgroundResFreq()

double ColumnResidueProfile::getBackgroundResFreq ( char  res)

◆ getEaaCode()

static char ColumnResidueProfile::getEaaCode ( char  stdCode)

◆ getIndexByConsensus()

int ColumnResidueProfile::getIndexByConsensus ( ) const

◆ getMostFrequentResidue()

char ColumnResidueProfile::getMostFrequentResidue ( int count) const

Definition at line 105 of file cuResidueProfile.cpp.

References i, m_residueRowsMap, m_residues, and max().

◆ getNcbiStdCode()

unsigned char ColumnResidueProfile::getNcbiStdCode ( char  eaa)

◆ getResidueByRow()

unsigned char ColumnResidueProfile::getResidueByRow ( int  row)

Definition at line 210 of file cuResidueProfile.cpp.

References findRow(), getNcbiStdCode(), and row.

Referenced by MasterColumnCounter::read().

◆ getResiduesByRow()

void ColumnResidueProfile::getResiduesByRow ( vector< char > &  residues,
bool  byNcbiStd = true 
) const

◆ getResidueTypeCount()

int ColumnResidueProfile::getResidueTypeCount ( ) const

Definition at line 71 of file cuResidueProfile.hpp.

Referenced by ResidueProfiles::calculateRowWeights().

◆ getSumCount()

int ColumnResidueProfile::getSumCount ( ) const

◆ isAligned() [1/2]

bool ColumnResidueProfile::isAligned ( char  residue,
int  row 
) const

◆ isAligned() [2/2]

bool ColumnResidueProfile::isAligned ( int  row)

Definition at line 234 of file cuResidueProfile.cpp.

References findRow(), and row.

◆ isAllRowsAligned()

bool ColumnResidueProfile::isAllRowsAligned ( ) const

◆ reweightColumnByRowWeights()

double ColumnResidueProfile::reweightColumnByRowWeights ( const vector< double > &  rowWeights,
char &  heaviestResidue 
) const

◆ setIndexByConsensus()

void ColumnResidueProfile::setIndexByConsensus ( int  col)

Definition at line 69 of file cuResidueProfile.hpp.

Referenced by ResidueProfiles::adjustConsensusAndGuide().

◆ sumUpColumnWeightsByRow()

double ColumnResidueProfile::sumUpColumnWeightsByRow ( vector< double > &  rowWeights,
bool  countGap,
int  numRows 
) const

◆ useDefaultBackgroundResFreq()

void ColumnResidueProfile::useDefaultBackgroundResFreq ( )

Definition at line 257 of file cuResidueProfile.cpp.

References m_backgroundResFreq.

Member Data Documentation

◆ m_backgroundResFreq

map< char, double > ColumnResidueProfile::m_backgroundResFreq

Definition at line 88 of file cuResidueProfile.hpp.

Referenced by useDefaultBackgroundResFreq().

◆ m_indexByConsensus

int ColumnResidueProfile::m_indexByConsensus

Definition at line 92 of file cuResidueProfile.hpp.

◆ m_masterIn

bool ColumnResidueProfile::m_masterIn

Definition at line 84 of file cuResidueProfile.hpp.

Referenced by addOccurence().

◆ m_residueRowsMap

ResidueRowsMap ColumnResidueProfile::m_residueRowsMap

◆ m_residues

const string ColumnResidueProfile::m_residues = "-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"

◆ m_residuesByRow

vector<ResidueRowsMap::iterator*> ColumnResidueProfile::m_residuesByRow

Definition at line 87 of file cuResidueProfile.hpp.

Referenced by addOccurence(), and ~ColumnResidueProfile().

◆ m_residueTypeCount

int ColumnResidueProfile::m_residueTypeCount

Definition at line 91 of file cuResidueProfile.hpp.

Referenced by addOccurence(), and calculateColumnWeight().

The documentation for this class was generated from the following files:
Modified on Mon Jun 24 05:19:25 2024 by rev. 669887