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CAnyIntron Class Reference

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

+ Inheritance diagram for CAnyIntron:
+ Collaboration diagram for CAnyIntron:

Classes

class  CSIntronScore
 

Public Member Functions

CHIntronScore Getw000 ()
 
CHIntronScore Getv000 ()
 
CHIntronScore Geth000 ()
 
CHIntronScore Getfh000 ()
 
CHIntronScore Getfv000 ()
 
CHIntronScore Getw111 ()
 
CHIntronScore Getfv111 ()
 
CHIntronScore Getw012 ()
 
CHIntronScore Geth012 ()
 
CHIntronScore Getw021 ()
 
CHIntronScore Geth021 ()
 
 CAnyIntron (int j1, char amin1, const CAlignInfo &prev, const CAlignInfo &cur, const CNSeq &nseq_ori, const CProSplignScaledScoring &scoring)
 
void SimpleNucStep (const CProSplignScaledScoring scoring)
 
void NucStep (const CProSplignScaledScoring scoring, const CSubstMatrix &matrix)
 
void AddW1 (const CProSplignScaledScoring scoring)
 
void AddW2 (const CProSplignScaledScoring scoring, const CSubstMatrix &matrix)
 
CHIntronScore GetW1 (const CSubstMatrix &matrix)
 
CHIntronScore GetW2 ()
 

Public Attributes

CSIntronScore sw012
 
CSIntronScore sh012
 
CSIntronScore sfv111
 
CSIntronScore sw111
 
CSIntronScore sw021
 
CSIntronScore sh021
 
CSIntronScore sw000
 
CSIntronScore sh000
 
CSIntronScore sv000
 
CSIntronScore sfv000
 
CSIntronScore sfh000
 

Protected Attributes

CHIntronScore swa
 
CHIntronScore swt
 
CHIntronScore swg
 
CHIntronScore swc
 
CHIntronScore swn
 
CHIntronScore sea
 
CHIntronScore set
 
CHIntronScore seg
 
CHIntronScore sec
 
CHIntronScore sen
 
const intesc
 
int j
 
char amin
 
const CNSeqnseq
 

Detailed Description

Definition at line 60 of file intron.hpp.

Constructor & Destructor Documentation

◆ CAnyIntron()

CAnyIntron::CAnyIntron ( int  j1,
char  amin1,
const CAlignInfo prev,
const CAlignInfo cur,
const CNSeq nseq_ori,
const CProSplignScaledScoring scoring 
)
inline

Member Function Documentation

◆ AddW1()

void CAnyIntron::AddW1 ( const CProSplignScaledScoring  scoring)

Definition at line 74 of file intron.cpp.

References esc, j, CProSplignScaledScoring::lmin, nA, nC, nG, nseq, nT, swa, swc, swg, swn, and swt.

Referenced by NucStep(), and CIntron::NucStep().

◆ AddW2()

void CAnyIntron::AddW2 ( const CProSplignScaledScoring  scoring,
const CSubstMatrix matrix 
)

Definition at line 111 of file intron.cpp.

References amin, esc, j, CProSplignScaledScoring::lmin, CSubstMatrix::MultScore(), nA, nC, nG, nN, nseq, nT, sea, sec, seg, and sen.

Referenced by NucStep(), and CIntron::NucStep().

◆ Getfh000()

CHIntronScore CAnyIntron::Getfh000 ( )
inline

Definition at line 115 of file intron.hpp.

◆ Getfv000()

CHIntronScore CAnyIntron::Getfv000 ( )
inline

Definition at line 116 of file intron.hpp.

◆ Getfv111()

CHIntronScore CAnyIntron::Getfv111 ( )
inline

Definition at line 126 of file intron.hpp.

◆ Geth000()

CHIntronScore CAnyIntron::Geth000 ( )
inline

Definition at line 114 of file intron.hpp.

◆ Geth012()

CHIntronScore CAnyIntron::Geth012 ( )
inline

Definition at line 128 of file intron.hpp.

◆ Geth021()

CHIntronScore CAnyIntron::Geth021 ( )
inline

Definition at line 130 of file intron.hpp.

◆ Getv000()

CHIntronScore CAnyIntron::Getv000 ( )
inline

Definition at line 113 of file intron.hpp.

◆ Getw000()

CHIntronScore CAnyIntron::Getw000 ( )
inline

Definition at line 112 of file intron.hpp.

◆ Getw012()

CHIntronScore CAnyIntron::Getw012 ( )
inline

Definition at line 127 of file intron.hpp.

◆ Getw021()

CHIntronScore CAnyIntron::Getw021 ( )
inline

Definition at line 129 of file intron.hpp.

◆ GetW1()

CHIntronScore CAnyIntron::GetW1 ( const CSubstMatrix matrix)
inline

Definition at line 162 of file intron.hpp.

References amin, j, CSubstMatrix::MultScore(), nA, nC, nG, nN, nseq, nT, swa, swc, swg, swn, swt, and tmp.

Referenced by CIntron::GetW1(), and CBestIntron::GetW1().

◆ Getw111()

CHIntronScore CAnyIntron::Getw111 ( )
inline

Definition at line 125 of file intron.hpp.

◆ GetW2()

CHIntronScore CAnyIntron::GetW2 ( )
inline

Definition at line 182 of file intron.hpp.

References j, nA, nC, nG, nseq, nT, sea, sec, seg, and sen.

◆ NucStep()

void CAnyIntron::NucStep ( const CProSplignScaledScoring  scoring,
const CSubstMatrix matrix 
)

◆ SimpleNucStep()

void CAnyIntron::SimpleNucStep ( const CProSplignScaledScoring  scoring)

Definition at line 47 of file intron.cpp.

Referenced by NucStep(), and CIntron::SimpleNucStep().

Member Data Documentation

◆ amin

char CAnyIntron::amin
protected

Definition at line 93 of file intron.hpp.

Referenced by AddW2(), CAnyIntron(), and GetW1().

◆ esc

const int* CAnyIntron::esc
protected

Definition at line 91 of file intron.hpp.

Referenced by AddW1(), AddW2(), and CAnyIntron().

◆ j

int CAnyIntron::j
protected

◆ nseq

const CNSeq& CAnyIntron::nseq
protected

Definition at line 94 of file intron.hpp.

Referenced by AddW1(), AddW2(), GetW1(), GetW2(), CIntron::IsDon(), and CIntron::NotAcs().

◆ sea

CHIntronScore CAnyIntron::sea
protected

Definition at line 90 of file intron.hpp.

Referenced by AddW2(), and GetW2().

◆ sec

CHIntronScore CAnyIntron::sec
protected

Definition at line 90 of file intron.hpp.

Referenced by AddW2(), and GetW2().

◆ seg

CHIntronScore CAnyIntron::seg
protected

Definition at line 90 of file intron.hpp.

Referenced by AddW2(), and GetW2().

◆ sen

CHIntronScore CAnyIntron::sen
protected

Definition at line 90 of file intron.hpp.

Referenced by AddW2(), and GetW2().

◆ set

CHIntronScore CAnyIntron::set
protected

Definition at line 90 of file intron.hpp.

◆ sfh000

CSIntronScore CAnyIntron::sfh000

Definition at line 103 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sfv000

CSIntronScore CAnyIntron::sfv000

Definition at line 103 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sfv111

CSIntronScore CAnyIntron::sfv111

Definition at line 101 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sh000

CSIntronScore CAnyIntron::sh000

Definition at line 103 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sh012

CSIntronScore CAnyIntron::sh012

Definition at line 99 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sh021

CSIntronScore CAnyIntron::sh021

Definition at line 101 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sv000

CSIntronScore CAnyIntron::sv000

Definition at line 103 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sw000

CSIntronScore CAnyIntron::sw000

Definition at line 103 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sw012

CSIntronScore CAnyIntron::sw012

Definition at line 99 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sw021

CSIntronScore CAnyIntron::sw021

Definition at line 101 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ sw111

CSIntronScore CAnyIntron::sw111

Definition at line 101 of file intron.hpp.

Referenced by CAnyIntron(), NucStep(), and CIntron::NucStep().

◆ swa

CHIntronScore CAnyIntron::swa
protected

Definition at line 89 of file intron.hpp.

Referenced by AddW1(), and GetW1().

◆ swc

CHIntronScore CAnyIntron::swc
protected

Definition at line 89 of file intron.hpp.

Referenced by AddW1(), and GetW1().

◆ swg

CHIntronScore CAnyIntron::swg
protected

Definition at line 89 of file intron.hpp.

Referenced by AddW1(), and GetW1().

◆ swn

CHIntronScore CAnyIntron::swn
protected

Definition at line 89 of file intron.hpp.

Referenced by AddW1(), and GetW1().

◆ swt

CHIntronScore CAnyIntron::swt
protected

Definition at line 89 of file intron.hpp.

Referenced by AddW1(), and GetW1().


The documentation for this class was generated from the following files:
Modified on Thu Jun 13 17:30:21 2024 by modify_doxy.py rev. 669887