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PssmScorer Class Reference

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

+ Collaboration diagram for PssmScorer:

Public Member Functions

 PssmScorer (CRef< CPssmWithParameters > pssm)
 
int score (const CRef< CSeq_align > align, const CRef< CBioseq > bioseq)
 
int score (BlockModelPair &bmp, const CRef< CBioseq > bioseq)
 
const vector< vector< int > > & getRawScores () const
 

Private Member Functions

int scoreOneColumn (int col, char aa)
 

Private Attributes

CRef< CPssmWithParametersm_pssm
 
vector< vector< int > > m_scoresFromPssm
 

Detailed Description

Definition at line 48 of file cuPssmScorer.hpp.

Constructor & Destructor Documentation

◆ PssmScorer()

PssmScorer::PssmScorer ( CRef< CPssmWithParameters pssm)

Definition at line 45 of file cuPssmScorer.cpp.

Member Function Documentation

◆ getRawScores()

const vector< vector<int> >& PssmScorer::getRawScores ( ) const
inline

Definition at line 57 of file cuPssmScorer.hpp.

◆ score() [1/2]

int PssmScorer::score ( BlockModelPair bmp,
const CRef< CBioseq bioseq 
)

◆ score() [2/2]

int PssmScorer::score ( const CRef< CSeq_align align,
const CRef< CBioseq bioseq 
)

Definition at line 76 of file cuPssmScorer.cpp.

References bmp.

Referenced by findHighestScoringRowByPssm(), and score().

◆ scoreOneColumn()

int PssmScorer::scoreOneColumn ( int  col,
char  aa 
)
inlineprivate

Definition at line 107 of file cuPssmScorer.cpp.

References m_scoresFromPssm.

Referenced by score().

Member Data Documentation

◆ m_pssm

CRef< CPssmWithParameters > PssmScorer::m_pssm
private

Definition at line 61 of file cuPssmScorer.hpp.

Referenced by score().

◆ m_scoresFromPssm

vector< vector<int> > PssmScorer::m_scoresFromPssm
private

Definition at line 62 of file cuPssmScorer.hpp.

Referenced by score(), and scoreOneColumn().


The documentation for this class was generated from the following files:
Modified on Tue Feb 27 05:53:19 2024 by modify_doxy.py rev. 669887