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CFIntron Class Reference

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#include "intron.hpp"
(Private to src/algo/align/prosplign.)

+ Collaboration diagram for CFIntron:

Public Member Functions

void InitRowScores (CAlignRow *row, vector< int > &prevw, int j)
 
 CFIntron (const CNSeq &nseq, const CProSplignScaledScoring scoring)
 
const CBestIStep (int j, const CProSplignScaledScoring &scoring, const CFastIScore &fiscore)
 
int GetWlen (int j, const CProSplignScaledScoring &scoring) const
 
int GetVlen (int j, const CProSplignScaledScoring &scoring) const
 
int GetH1len (int j, const CProSplignScaledScoring &scoring) const
 
int GetH2len (int j, const CProSplignScaledScoring &scoring) const
 
int GetH3len (int j, const CProSplignScaledScoring &scoring) const
 
int GetW2len (int j, const CProSplignScaledScoring &scoring) const
 
int GetW1len (int j, const CProSplignScaledScoring &scoring) const
 

Static Public Member Functions

static int Getlen (const EAccType &at, int sc, const CHIntronScore &sc_any, const CHIntronScore &sc_at, const CHIntronScore &sc_gt, const CHIntronScore &sc_gc, int j, const CProSplignScaledScoring &scoring)
 

Private Member Functions

CFIntronoperator= (const CFIntron &)
 
 CFIntron (const CFIntron &)
 
void InitW12s (int j, const CProSplignScaledScoring &scoring, const CFastIScore &fiscore)
 
void BestScAny (const CProSplignScaledScoring &scoring)
 
void BestScCon (const CFIntronDon &don, int cost, int j, const CProSplignScaledScoring &scoring)
 
int BestSc1 (const CFIntronDon &don, int j, const CProSplignScaledScoring &scoring) const
 
int GetLen1 (int sc, const CFIntronDon &don, int j, const CProSplignScaledScoring &scoring) const
 
void AddDon1 (CFIntronDon &don, Nucleotides &nuc, int j, const CProSplignScaledScoring &scoring)
 
void AddDon1 (Nucleotides &nuc, int j, const CProSplignScaledScoring &scoring)
 
void AddDon2 (int j, const CProSplignScaledScoring &scoring)
 
void AddDon2 (CFIntronDon &don, int j, const CProSplignScaledScoring &scoring)
 
void AddDon (int j, const CProSplignScaledScoring &scoring)
 
void AddDon (CFIntronDon &don, int j, const CProSplignScaledScoring &scoring)
 

Static Private Member Functions

static EDonType GetDonType (char nuc1, char nuc2)
 
static EAccType GetAccType (char nuc1, char nuc2)
 
static void AddDonAny (int sc, CHIntronScore &bsc, int j, const CProSplignScaledScoring &scoring)
 
static void AddDonCon (int sc, CHIntronScore &bsc, int j, const CProSplignScaledScoring &scoring)
 

Private Attributes

CBestI m_bei
 
CFIntronDon m_gt
 
CFIntronDon m_gc
 
CFIntronDon m_at
 
CFIntronDon m_any
 
int m_w1s [5]
 
int m_w2s [5]
 
vector< CFIntornDatam_data
 
CFIntornDatam_cd
 
intm_v
 
intm_h1
 
intm_h2
 
intm_h3
 
intm_w
 
intm_w12
 
const CNSeqm_nseq
 

Detailed Description

Definition at line 447 of file intron.hpp.

Constructor & Destructor Documentation

◆ CFIntron() [1/2]

CFIntron::CFIntron ( const CFIntron )
private

◆ CFIntron() [2/2]

CFIntron::CFIntron ( const CNSeq nseq,
const CProSplignScaledScoring  scoring 
)

Member Function Documentation

◆ AddDon() [1/2]

void CFIntron::AddDon ( CFIntronDon don,
int  j,
const CProSplignScaledScoring scoring 
)
inlineprivate

◆ AddDon() [2/2]

void CFIntron::AddDon ( int  j,
const CProSplignScaledScoring scoring 
)
inlineprivate

◆ AddDon1() [1/2]

void CFIntron::AddDon1 ( CFIntronDon don,
Nucleotides nuc,
int  j,
const CProSplignScaledScoring scoring 
)
inlineprivate

Definition at line 560 of file intron.hpp.

References CFIntronDon::m_w1, and nuc.

◆ AddDon1() [2/2]

void CFIntron::AddDon1 ( Nucleotides nuc,
int  j,
const CProSplignScaledScoring scoring 
)
inlineprivate

Definition at line 564 of file intron.hpp.

References CFIntronDon::m_w1, and nuc.

◆ AddDon2() [1/2]

void CFIntron::AddDon2 ( CFIntronDon don,
int  j,
const CProSplignScaledScoring scoring 
)
inlineprivate

Definition at line 575 of file intron.hpp.

References CFIntronDon::m_w2, nA, nC, nG, nN, and nT.

◆ AddDon2() [2/2]

void CFIntron::AddDon2 ( int  j,
const CProSplignScaledScoring scoring 
)
inlineprivate

Definition at line 567 of file intron.hpp.

References CFIntronDon::m_w2, nA, nC, nG, nN, and nT.

◆ AddDonAny()

static void CFIntron::AddDonAny ( int  sc,
CHIntronScore bsc,
int  j,
const CProSplignScaledScoring scoring 
)
inlinestaticprivate

Definition at line 548 of file intron.hpp.

References CProSplignScaledScoring::ie.

◆ AddDonCon()

static void CFIntron::AddDonCon ( int  sc,
CHIntronScore bsc,
int  j,
const CProSplignScaledScoring scoring 
)
inlinestaticprivate

Definition at line 554 of file intron.hpp.

References CProSplignScaledScoring::ie.

◆ BestSc1()

int CFIntron::BestSc1 ( const CFIntronDon don,
int  j,
const CProSplignScaledScoring scoring 
) const
inlineprivate

Definition at line 514 of file intron.hpp.

References CProSplignScaledScoring::ie, CFIntronDon::m_w1, and tmp.

◆ BestScAny()

void CFIntron::BestScAny ( const CProSplignScaledScoring scoring)
inlineprivate

◆ BestScCon()

void CFIntron::BestScCon ( const CFIntronDon don,
int  cost,
int  j,
const CProSplignScaledScoring scoring 
)
inlineprivate

◆ GetAccType()

static EAccType CFIntron::GetAccType ( char  nuc1,
char  nuc2 
)
inlinestaticprivate

Definition at line 469 of file intron.hpp.

References eAC, eAG, eANYa, nA, nC, and nG.

Referenced by CFIntron().

◆ GetDonType()

static EDonType CFIntron::GetDonType ( char  nuc1,
char  nuc2 
)
inlinestaticprivate

Definition at line 462 of file intron.hpp.

References eANY, eAT, eGC, eGT, nA, nC, nG, and nT.

Referenced by CFIntron().

◆ GetH1len()

int CFIntron::GetH1len ( int  j,
const CProSplignScaledScoring scoring 
) const
inline

Definition at line 734 of file intron.hpp.

References CBestI::h1, CFIntornData::m_at, and CFIntronDon::m_h1.

Referenced by AlignFNog(), and FindFGapIntronNog().

◆ GetH2len()

int CFIntron::GetH2len ( int  j,
const CProSplignScaledScoring scoring 
) const
inline

Definition at line 735 of file intron.hpp.

References CBestI::h2, CFIntornData::m_at, and CFIntronDon::m_h2.

Referenced by AlignFNog(), and FindFGapIntronNog().

◆ GetH3len()

int CFIntron::GetH3len ( int  j,
const CProSplignScaledScoring scoring 
) const
inline

Definition at line 736 of file intron.hpp.

References CBestI::h3, CFIntornData::m_at, and CFIntronDon::m_h3.

Referenced by AlignFNog(), and FindFGapIntronNog().

◆ Getlen()

static int CFIntron::Getlen ( const EAccType at,
int  sc,
const CHIntronScore sc_any,
const CHIntronScore sc_at,
const CHIntronScore sc_gt,
const CHIntronScore sc_gc,
int  j,
const CProSplignScaledScoring scoring 
)
inlinestatic

◆ GetLen1()

int CFIntron::GetLen1 ( int  sc,
const CFIntronDon don,
int  j,
const CProSplignScaledScoring scoring 
) const
inlineprivate

◆ GetVlen()

int CFIntron::GetVlen ( int  j,
const CProSplignScaledScoring scoring 
) const
inline

Definition at line 733 of file intron.hpp.

References CFIntornData::m_at, CFIntronDon::m_v, and CBestI::v.

Referenced by AlignFNog(), and FindFGapIntronNog().

◆ GetW1len()

int CFIntron::GetW1len ( int  j,
const CProSplignScaledScoring scoring 
) const
inline

◆ GetW2len()

int CFIntron::GetW2len ( int  j,
const CProSplignScaledScoring scoring 
) const
inline

◆ GetWlen()

int CFIntron::GetWlen ( int  j,
const CProSplignScaledScoring scoring 
) const
inline

Definition at line 732 of file intron.hpp.

References CFIntornData::m_at, CFIntronDon::m_w, and CBestI::w.

Referenced by AlignFNog(), and FindFGapIntronNog().

◆ InitRowScores()

void CFIntron::InitRowScores ( CAlignRow row,
vector< int > &  prevw,
int  j 
)

Definition at line 215 of file intron.cpp.

References i, m_any, m_at, m_cd, m_data, m_gc, m_gt, m_h1, m_h2, m_h3, m_v, m_w, m_w12, m_w1s, m_w2s, CFIntronDon::Reset(), and row.

Referenced by AlignFNog(), and FindFGapIntronNog().

◆ InitW12s()

void CFIntron::InitW12s ( int  j,
const CProSplignScaledScoring scoring,
const CFastIScore fiscore 
)
inlineprivate

Definition at line 476 of file intron.hpp.

References CFastIScore::GetScore(), CProSplignScaledScoring::lmin, nA, nC, nG, nN, and nT.

◆ operator=()

CFIntron& CFIntron::operator= ( const CFIntron )
private

◆ Step()

const CBestI& CFIntron::Step ( int  j,
const CProSplignScaledScoring scoring,
const CFastIScore fiscore 
)
inline

Member Data Documentation

◆ m_any

CFIntronDon CFIntron::m_any
private

Definition at line 451 of file intron.hpp.

Referenced by InitRowScores().

◆ m_at

CFIntronDon CFIntron::m_at
private

Definition at line 451 of file intron.hpp.

Referenced by InitRowScores().

◆ m_bei

CBestI CFIntron::m_bei
private

Definition at line 450 of file intron.hpp.

◆ m_cd

CFIntornData* CFIntron::m_cd
private

Definition at line 454 of file intron.hpp.

Referenced by InitRowScores().

◆ m_data

vector<CFIntornData> CFIntron::m_data
private

Definition at line 453 of file intron.hpp.

Referenced by CFIntron(), and InitRowScores().

◆ m_gc

CFIntronDon CFIntron::m_gc
private

Definition at line 451 of file intron.hpp.

Referenced by InitRowScores().

◆ m_gt

CFIntronDon CFIntron::m_gt
private

Definition at line 451 of file intron.hpp.

Referenced by InitRowScores().

◆ m_h1

int * CFIntron::m_h1
private

Definition at line 455 of file intron.hpp.

Referenced by InitRowScores().

◆ m_h2

int * CFIntron::m_h2
private

Definition at line 455 of file intron.hpp.

Referenced by InitRowScores().

◆ m_h3

int * CFIntron::m_h3
private

Definition at line 455 of file intron.hpp.

Referenced by InitRowScores().

◆ m_nseq

const CNSeq& CFIntron::m_nseq
private

Definition at line 456 of file intron.hpp.

◆ m_v

int* CFIntron::m_v
private

Definition at line 455 of file intron.hpp.

Referenced by InitRowScores().

◆ m_w

int * CFIntron::m_w
private

Definition at line 455 of file intron.hpp.

Referenced by InitRowScores().

◆ m_w12

int * CFIntron::m_w12
private

Definition at line 455 of file intron.hpp.

Referenced by InitRowScores().

◆ m_w1s

int CFIntron::m_w1s[5]
private

Definition at line 452 of file intron.hpp.

Referenced by InitRowScores().

◆ m_w2s

int CFIntron::m_w2s[5]
private

Definition at line 452 of file intron.hpp.

Referenced by InitRowScores().


The documentation for this class was generated from the following files:
Modified on Sat May 18 11:41:14 2024 by modify_doxy.py rev. 669887